Variant rs6116 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_000624.6(SERPINA5):c.1107A>C(p.Ile369=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 1,613,828 control chromosomes in the GnomAD database, including 172,299 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.

Frequency

Genomes: 𝑓 0.40 ( 12920 hom., cov: 32)

Exomes 𝑓: 0.46 ( 159379 hom. )

Consequence

SERPINA5
NM_000624.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00200

Variant links:

Genes affected

SERPINA5 (HGNC:8723): (serpin family A member 5) The protein encoded by this gene is a member of the serpin family of proteins, a group of proteins that inhibit serine proteases. This gene is one in a cluster of serpin genes located on the q arm of chromosome 14. This family member is a glycoprotein that can inhibit several serine proteases, including protein C and various plasminogen activators and kallikreins, and it thus plays diverse roles in hemostasis and thrombosis in multiple organs. [provided by RefSeq, Aug 2012]

SERPINA5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP7

Synonymous conserved (PhyloP=-0.002 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SERPINA5	NM_000624.6 linkuse as main transcript	c.1107A>C	p.Ile369=	synonymous_variant	6/6	ENST00000329597.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
SERPINA5	ENST00000329597.12 linkuse as main transcript	c.1107A>C	p.Ile369=	synonymous_variant	6/6	1	NM_000624.6	P1
SERPINA5	ENST00000554276.1 linkuse as main transcript	c.1107A>C	p.Ile369=	synonymous_variant	5/5	1		P1
SERPINA5	ENST00000553780.5 linkuse as main transcript	c.1107A>C	p.Ile369=	synonymous_variant	7/7	5		P1
SERPINA5	ENST00000554866.5 linkuse as main transcript	c.1107A>C	p.Ile369=	synonymous_variant	5/5	5		P1

Frequencies

GnomAD3 genomes

AF:

0.396

AC:

60114

AN:

151930

Hom.:

12920

Cov.:

show subpopulations

Gnomad AFR

AF:

0.287

Gnomad AMI

AF:

0.318

Gnomad AMR

AF:

0.313

Gnomad ASJ

AF:

0.536

Gnomad EAS

AF:

0.0865

Gnomad SAS

AF:

0.338

Gnomad FIN

AF:

0.513

Gnomad MID

AF:

0.538

Gnomad NFE

AF:

0.483

Gnomad OTH

AF:

0.405

GnomAD3 exomes

AF:

0.391

AC:

98140

AN:

251260

Hom.:

21777

AF XY:

0.402

AC XY:

54640

AN XY:

135808

show subpopulations

Gnomad AFR exome

AF:

0.285

Gnomad AMR exome

AF:

0.213

Gnomad ASJ exome

AF:

0.535

Gnomad EAS exome

AF:

0.0757

Gnomad SAS exome

AF:

0.353

Gnomad FIN exome

AF:

0.508

Gnomad NFE exome

AF:

0.483

Gnomad OTH exome

AF:

0.437

GnomAD4 exome

AF:

0.457

AC:

668604

AN:

1461778

Hom.:

159379

Cov.:

AF XY:

0.457

AC XY:

332018

AN XY:

727184

show subpopulations

Gnomad4 AFR exome

AF:

0.285

Gnomad4 AMR exome

AF:

0.226

Gnomad4 ASJ exome

AF:

0.532

Gnomad4 EAS exome

AF:

0.0887

Gnomad4 SAS exome

AF:

0.362

Gnomad4 FIN exome

AF:

0.511

Gnomad4 NFE exome

AF:

0.489

Gnomad4 OTH exome

AF:

0.440

GnomAD4 genome

AF:

0.395

AC:

60123

AN:

152050

Hom.:

12920

Cov.:

AF XY:

0.394

AC XY:

29257

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.287

Gnomad4 AMR

AF:

0.313

Gnomad4 ASJ

AF:

0.536

Gnomad4 EAS

AF:

0.0864

Gnomad4 SAS

AF:

0.340

Gnomad4 FIN

AF:

0.513

Gnomad4 NFE

AF:

0.483

Gnomad4 OTH

AF:

0.400

Alfa

AF:

0.454

Hom.:

20335

Bravo

AF:

0.374

Asia WGS

AF:

0.195

AC:

684

AN:

3478

EpiCase

AF:

0.489

EpiControl

AF:

0.492

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.1

DANN

Benign

0.58

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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