Variant 1-31424709-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_178865.5(SERINC2):c.228C>T(p.Ala76=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0035 in 1,603,746 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0026 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0036 ( 20 hom. )

Consequence

SERINC2
NM_178865.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.299

Variant links:

Genes affected

SERINC2 (HGNC:23231): (serine incorporator 2) Predicted to be involved in several processes, including phosphatidylserine metabolic process; positive regulation of CDP-diacylglycerol-serine O-phosphatidyltransferase activity; and positive regulation of serine C-palmitoyltransferase activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

SERINC2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 1-31424709-C-T is Benign according to our data. Variant chr1-31424709-C-T is described in ClinVar as [Benign]. Clinvar id is 788760.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.299 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 20 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SERINC2	NM_178865.5 linkuse as main transcript	c.228C>T	p.Ala76=	synonymous_variant	3/10	ENST00000373709.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SERINC2	ENST00000373709.8 linkuse as main transcript	c.228C>T	p.Ala76=	synonymous_variant	3/10	1	NM_178865.5	P1	Q96SA4-1

Frequencies

GnomAD3 genomes

AF:

0.00261

AC:

397

AN:

152166

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00101

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00216

Gnomad ASJ

AF:

0.00518

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00332

Gnomad FIN

AF:

0.00104

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00385

Gnomad OTH

AF:

0.00431

GnomAD3 exomes

AF:

0.00273

AC:

625

AN:

228804

Hom.:

AF XY:

0.00310

AC XY:

385

AN XY:

124020

show subpopulations

Gnomad AFR exome

AF:

0.000484

Gnomad AMR exome

AF:

0.000833

Gnomad ASJ exome

AF:

0.00412

Gnomad EAS exome

AF:

0.0000584

Gnomad SAS exome

AF:

0.00446

Gnomad FIN exome

AF:

0.00110

Gnomad NFE exome

AF:

0.00381

Gnomad OTH exome

AF:

0.00250

GnomAD4 exome

AF:

0.00359

AC:

5216

AN:

1451462

Hom.:

Cov.:

AF XY:

0.00370

AC XY:

2671

AN XY:

721174

show subpopulations

Gnomad4 AFR exome

AF:

0.00111

Gnomad4 AMR exome

AF:

0.000998

Gnomad4 ASJ exome

AF:

0.00415

Gnomad4 EAS exome

AF:

0.0000255

Gnomad4 SAS exome

AF:

0.00433

Gnomad4 FIN exome

AF:

0.00107

Gnomad4 NFE exome

AF:

0.00389

Gnomad4 OTH exome

AF:

0.00439

GnomAD4 genome

AF:

0.00261

AC:

397

AN:

152284

Hom.:

Cov.:

AF XY:

0.00234

AC XY:

174

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00101

Gnomad4 AMR

AF:

0.00216

Gnomad4 ASJ

AF:

0.00518

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00332

Gnomad4 FIN

AF:

0.00104

Gnomad4 NFE

AF:

0.00385

Gnomad4 OTH

AF:

0.00427

Alfa

AF:

0.00270

Hom.:

Bravo

AF:

0.00243

Asia WGS

AF:

0.00173

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jul 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

7.5

DANN

Benign

0.31

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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