chr14-94382864-C-T

Position:

chr14-94382864-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000295.5(SERPINA1):c.374G>A(p.Arg125His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 1,614,092 control chromosomes in the GnomAD database, including 21,879 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 1593 hom., cov: 33)

Exomes 𝑓: 0.16 ( 20286 hom. )

Consequence

SERPINA1
NM_000295.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:12O:2

Conservation

PhyloP100: -0.566

Variant links:

Genes affected

SERPINA1 (HGNC:8941): (serpin family A member 1) The protein encoded by this gene is a serine protease inhibitor belonging to the serpin superfamily whose targets include elastase, plasmin, thrombin, trypsin, chymotrypsin, and plasminogen activator. This protein is produced in the liver, the bone marrow, by lymphocytic and monocytic cells in lymphoid tissue, and by the Paneth cells of the gut. Defects in this gene are associated with chronic obstructive pulmonary disease, emphysema, and chronic liver disease. Several transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Aug 2020]

SERPINA1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0047332942).

BP6

Variant 14-94382864-C-T is Benign according to our data. Variant chr14-94382864-C-T is described in ClinVar as [Benign]. Clinvar id is 17957.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-94382864-C-T is described in Lovd as [Benign]. Variant chr14-94382864-C-T is described in Lovd as [Pathogenic].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SERPINA1	NM_000295.5 linkuse as main transcript	c.374G>A	p.Arg125His	missense_variant	2/5	ENST00000393087.9	NP_000286.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SERPINA1	ENST00000393087.9 linkuse as main transcript	c.374G>A	p.Arg125His	missense_variant	2/5	1	NM_000295.5	ENSP00000376802.4		P01009-1

Frequencies

GnomAD3 genomes

AF:

0.126

AC:

19194

AN:

152102

Hom.:

1583

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0391

Gnomad AMI

AF:

0.0936

Gnomad AMR

AF:

0.121

Gnomad ASJ

AF:

0.162

Gnomad EAS

AF:

0.220

Gnomad SAS

AF:

0.279

Gnomad FIN

AF:

0.121

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.161

Gnomad OTH

AF:

0.140

GnomAD3 exomes

AF:

0.160

AC:

40211

AN:

251352

Hom.:

3709

AF XY:

0.171

AC XY:

23199

AN XY:

135848

show subpopulations

Gnomad AFR exome

AF:

0.0332

Gnomad AMR exome

AF:

0.108

Gnomad ASJ exome

AF:

0.162

Gnomad EAS exome

AF:

0.207

Gnomad SAS exome

AF:

0.269

Gnomad FIN exome

AF:

0.121

Gnomad NFE exome

AF:

0.164

Gnomad OTH exome

AF:

0.166

GnomAD4 exome

AF:

0.161

AC:

235568

AN:

1461870

Hom.:

20286

Cov.:

AF XY:

0.166

AC XY:

120413

AN XY:

727230

show subpopulations

Gnomad4 AFR exome

AF:

0.0317

Gnomad4 AMR exome

AF:

0.110

Gnomad4 ASJ exome

AF:

0.159

Gnomad4 EAS exome

AF:

0.228

Gnomad4 SAS exome

AF:

0.268

Gnomad4 FIN exome

AF:

0.126

Gnomad4 NFE exome

AF:

0.158

Gnomad4 OTH exome

AF:

0.166

GnomAD4 genome

AF:

0.126

AC:

19215

AN:

152222

Hom.:

1593

Cov.:

AF XY:

0.128

AC XY:

9500

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.0393

Gnomad4 AMR

AF:

0.121

Gnomad4 ASJ

AF:

0.162

Gnomad4 EAS

AF:

0.221

Gnomad4 SAS

AF:

0.280

Gnomad4 FIN

AF:

0.121

Gnomad4 NFE

AF:

0.161

Gnomad4 OTH

AF:

0.147

Alfa

AF:

0.158

Hom.:

5022

Bravo

AF:

0.117

TwinsUK

AF:

0.160

AC:

593

ALSPAC

AF:

0.150

AC:

578

ESP6500AA

AF:

0.0363

AC:

160

ESP6500EA

AF:

0.165

AC:

1421

ExAC

AF:

0.163

AC:

19806

Asia WGS

AF:

0.237

AC:

825

AN:

3478

EpiCase

AF:

0.169

EpiControl

AF:

0.172

ClinVar

Significance: Benign

Submissions summary: Benign:12Other:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Alpha-1-antitrypsin deficiency

Benign:5

Benign, no assertion criteria provided	curation	Department of Laboratory Medicine and Genetics, Trillium Health Partners Credit Valley Hospital	Dec 08, 2014	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Mar 06, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Jan 27, 2022	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

not specified

Benign:4

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Aug 25, 2016	- -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Aug 06, 2015	p.Arg125His in exon 4 of SERPINA1: This variant is not expected to have clinical significance because it has been identified in 27% (4488/16512) of South Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitut e.org; dbSNP rs709932). -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	This variant is associated with the following publications: (PMID: 22426792, 27153395, 2339709, 20981092, 14551891, 2901226) -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Inborn genetic diseases

Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 02, 2017

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

PI M4

Other:1

other, no assertion criteria provided

literature only

OMIM

Jul 15, 2016

- -

PI M2

Other:1

other, no assertion criteria provided

literature only

OMIM

Jul 15, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.059

BayesDel_addAF

Benign

-0.55

BayesDel_noAF

Benign

-0.42

CADD

Benign

0.17

DANN

Benign

0.60

DEOGEN2

Benign

0.13

T;T;T;T;T;T;T;T;T;.;.;.;T

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.030

LIST_S2

Benign

0.10

.;.;.;T;.;.;.;.;.;T;T;.;.

MetaRNN

Benign

0.0047

T;T;T;T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-1.2

N;N;N;N;N;N;N;N;N;N;.;.;.

PrimateAI

Benign

0.18

PROVEAN

Benign

3.1

N;N;N;N;N;.;N;N;N;N;N;N;N

REVEL

Benign

0.24

Sift

Benign

1.0

T;T;T;T;T;.;T;T;T;T;T;T;T

Sift4G

Benign

1.0

T;T;T;T;T;.;T;T;T;T;.;.;.

Polyphen

0.0

B;B;B;B;B;B;B;B;B;B;.;.;.

Vest4

0.0070

MPC

0.051

ClinPred

0.0016

GERP RS

-2.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.075

gMVP

0.27

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over