Variant 14-94288467-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001100607.3(SERPINA10):c.811G>A(p.Gly271Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0114 in 1,614,006 control chromosomes in the GnomAD database, including 448 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.031 ( 198 hom., cov: 32)

Exomes 𝑓: 0.0094 ( 250 hom. )

Consequence

SERPINA10
NM_001100607.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.439

Variant links:

Genes affected

SERPINA10 (HGNC:15996): (serpin family A member 10) The protein encoded by this gene belongs to the serpin family. It is predominantly expressed in the liver and secreted in plasma. It inhibits the activity of coagulation factors Xa and XIa in the presence of protein Z, calcium and phospholipid. Mutations in this gene are associated with venous thrombosis. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, May 2010]

SERPINA10 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0016829967).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SERPINA10	NM_001100607.3 linkuse as main transcript	c.811G>A	p.Gly271Ser	missense_variant	3/5	ENST00000261994.9	NP_001094077.1	Q9UK55A0A024R6I6
SERPINA10	NM_016186.3 linkuse as main transcript	c.811G>A	p.Gly271Ser	missense_variant	3/5		NP_057270.1	Q9UK55A0A024R6I6
SERPINA10	XM_017021353.2 linkuse as main transcript	c.931G>A	p.Gly311Ser	missense_variant	4/6		XP_016876842.1	G3V2W1
SERPINA10	XM_005267733.6 linkuse as main transcript	c.811G>A	p.Gly271Ser	missense_variant	3/5		XP_005267790.1	Q9UK55A0A024R6I6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SERPINA10	ENST00000261994.9 linkuse as main transcript	c.811G>A	p.Gly271Ser	missense_variant	3/5	1	NM_001100607.3	ENSP00000261994.4	Q9UK55
SERPINA10	ENST00000554723.5 linkuse as main transcript	c.931G>A	p.Gly311Ser	missense_variant	3/5	1		ENSP00000450896.1	G3V2W1
SERPINA10	ENST00000393096.5 linkuse as main transcript	c.811G>A	p.Gly271Ser	missense_variant	3/5	1		ENSP00000376809.1	Q9UK55
SERPINA10	ENST00000554173.1 linkuse as main transcript	c.811G>A	p.Gly271Ser	missense_variant	2/4	1		ENSP00000450971.1	Q9UK55

Frequencies

GnomAD3 genomes

AF:

0.0307

AC:

4665

AN:

152000

Hom.:

200

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0898

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0161

Gnomad ASJ

AF:

0.0288

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0141

Gnomad FIN

AF:

0.00113

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.00654

Gnomad OTH

AF:

0.0244

GnomAD3 exomes

AF:

0.0142

AC:

3577

AN:

251456

Hom.:

AF XY:

0.0131

AC XY:

1775

AN XY:

135894

show subpopulations

Gnomad AFR exome

AF:

0.0920

Gnomad AMR exome

AF:

0.0123

Gnomad ASJ exome

AF:

0.0259

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0157

Gnomad FIN exome

AF:

0.00111

Gnomad NFE exome

AF:

0.00692

Gnomad OTH exome

AF:

0.0164

GnomAD4 exome

AF:

0.00940

AC:

13735

AN:

1461888

Hom.:

250

Cov.:

AF XY:

0.00947

AC XY:

6890

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.0927

Gnomad4 AMR exome

AF:

0.0124

Gnomad4 ASJ exome

AF:

0.0279

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.0162

Gnomad4 FIN exome

AF:

0.00150

Gnomad4 NFE exome

AF:

0.00584

Gnomad4 OTH exome

AF:

0.0156

GnomAD4 genome

AF:

0.0307

AC:

4668

AN:

152118

Hom.:

198

Cov.:

AF XY:

0.0299

AC XY:

2223

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.0897

Gnomad4 AMR

AF:

0.0161

Gnomad4 ASJ

AF:

0.0288

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0144

Gnomad4 FIN

AF:

0.00113

Gnomad4 NFE

AF:

0.00654

Gnomad4 OTH

AF:

0.0242

Alfa

AF:

0.0128

Hom.:

Bravo

AF:

0.0340

TwinsUK

AF:

0.00836

AC:

ALSPAC

AF:

0.00597

AC:

ESP6500AA

AF:

0.0865

AC:

381

ESP6500EA

AF:

0.00814

AC:

ExAC

AF:

0.0161

AC:

1954

Asia WGS

AF:

0.0120

AC:

AN:

3478

EpiCase

AF:

0.0110

EpiControl

AF:

0.00972

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.59

BayesDel_noAF

Benign

-0.54

CADD

Benign

DANN

Benign

0.66

DEOGEN2

Benign

0.099

T;.;T;T

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.0078

LIST_S2

Benign

0.36

.;T;T;.

MetaRNN

Benign

0.0017

T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-1.3

N;.;N;N

PrimateAI

Benign

0.25

PROVEAN

Benign

1.3

N;N;N;N

REVEL

Benign

0.12

Sift

Benign

0.24

T;T;T;T

Sift4G

Benign

0.13

T;T;T;T

Polyphen

0.11

B;.;B;B

Vest4

0.018

MPC

0.028

ClinPred

0.0027

GERP RS

-2.3

Varity_R

0.20

gMVP

0.54

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over