Variant rs2232710 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The ENST00000261994.9(SERPINA10):c.1151A>G(p.Gln384Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.01 in 1,613,922 control chromosomes in the GnomAD database, including 105 homozygotes. In-silico tool predicts 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q384P) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0078 ( 10 hom., cov: 32)

Exomes 𝑓: 0.010 ( 95 hom. )

Consequence

SERPINA10
ENST00000261994.9 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.37

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 -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0077571273).

BS2

High Homozygotes in GnomAd4 at 10 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
SERPINA10	NM_001100607.3 linkuse as main transcript	c.1151A>G	p.Gln384Arg	missense_variant	5/5	ENST00000261994.9	NP_001094077.1
SERPINA10	NM_016186.3 linkuse as main transcript	c.1151A>G	p.Gln384Arg	missense_variant	5/5		NP_057270.1
SERPINA10	XM_017021353.2 linkuse as main transcript	c.1271A>G	p.Gln424Arg	missense_variant	6/6		XP_016876842.1
SERPINA10	XM_005267733.6 linkuse as main transcript	c.1151A>G	p.Gln384Arg	missense_variant	5/5		XP_005267790.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
SERPINA10	ENST00000261994.9 linkuse as main transcript	c.1151A>G	p.Gln384Arg	missense_variant	5/5	1	NM_001100607.3	ENSP00000261994	A2
SERPINA10	ENST00000554723.5 linkuse as main transcript	c.1271A>G	p.Gln424Arg	missense_variant	5/5	1		ENSP00000450896	P4
SERPINA10	ENST00000393096.5 linkuse as main transcript	c.1151A>G	p.Gln384Arg	missense_variant	5/5	1		ENSP00000376809	A2
SERPINA10	ENST00000554173.1 linkuse as main transcript	c.1151A>G	p.Gln384Arg	missense_variant	4/4	1		ENSP00000450971	A2

Frequencies

GnomAD3 genomes

AF:

0.00782

AC:

1190

AN:

152246

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00181

Gnomad AMI

AF:

0.0285

Gnomad AMR

AF:

0.00249

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.0230

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0116

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00806

AC:

2013

AN:

249768

Hom.:

AF XY:

0.00836

AC XY:

1130

AN XY:

135122

show subpopulations

Gnomad AFR exome

AF:

0.00185

Gnomad AMR exome

AF:

0.00266

Gnomad ASJ exome

AF:

0.000398

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00317

Gnomad FIN exome

AF:

0.0186

Gnomad NFE exome

AF:

0.0120

Gnomad OTH exome

AF:

0.00735

GnomAD4 exome

AF:

0.0102

AC:

14960

AN:

1461558

Hom.:

Cov.:

AF XY:

0.00995

AC XY:

7232

AN XY:

727104

show subpopulations

Gnomad4 AFR exome

AF:

0.00158

Gnomad4 AMR exome

AF:

0.00293

Gnomad4 ASJ exome

AF:

0.000727

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00348

Gnomad4 FIN exome

AF:

0.0191

Gnomad4 NFE exome

AF:

0.0116

Gnomad4 OTH exome

AF:

0.00715

GnomAD4 genome

AF:

0.00781

AC:

1190

AN:

152364

Hom.:

Cov.:

AF XY:

0.00786

AC XY:

586

AN XY:

74510

show subpopulations

Gnomad4 AFR

AF:

0.00180

Gnomad4 AMR

AF:

0.00248

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00228

Gnomad4 FIN

AF:

0.0230

Gnomad4 NFE

AF:

0.0116

Gnomad4 OTH

AF:

0.00236

Alfa

AF:

0.0106

Hom.:

Bravo

AF:

0.00643

TwinsUK

AF:

0.0129

AC:

ALSPAC

AF:

0.0104

AC:

ESP6500AA

AF:

0.00227

AC:

ESP6500EA

AF:

0.0114

AC:

ExAC

AF:

0.00823

AC:

999

Asia WGS

AF:

0.00202

AC:

AN:

3478

EpiCase

AF:

0.0118

EpiControl

AF:

0.0103

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.44

BayesDel_addAF

Benign

-0.31

BayesDel_noAF

Benign

-0.21

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.44

T;.;T;T

Eigen

Benign

0.062

Eigen_PC

Benign

0.091

FATHMM_MKL

Uncertain

0.90

LIST_S2

Benign

0.57

.;T;T;.

MetaRNN

Benign

0.0078

T;T;T;T

MetaSVM

Uncertain

0.34

MutationAssessor

Uncertain

2.2

M;.;M;M

MutationTaster

Benign

1.0

D;D;D;D

PrimateAI

Benign

0.37

PROVEAN

Benign

-1.3

N;N;N;N

REVEL

Uncertain

0.40

Sift

Benign

0.13

T;T;T;T

Sift4G

Uncertain

0.051

T;D;T;T

Polyphen

0.23

B;.;B;B

Vest4

0.29

MVP

0.64

MPC

0.062

ClinPred

0.020

GERP RS

5.2

Varity_R

0.88

gMVP

0.75

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over