Variant rs731947 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001396050.1(SCART1):c.1758C>G(p.Asp586Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 542,090 control chromosomes in the GnomAD database, including 196,214 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 0.77 ( 46894 hom., cov: 35)

Exomes 𝑓: 0.87 ( 149320 hom. )

Consequence

SCART1
NM_001396050.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.304

Variant links:

Genes affected

SCART1 (HGNC:32411): (scavenger receptor family member expressed on T cells 1) Predicted to enable scavenger receptor activity. Predicted to be involved in endocytosis. Located in brush border and cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

SCART1 links:

SCART1 (HGNC:):

SCART1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.109885E-6).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCART1	NM_001396050.1 linkuse as main transcript	c.1758C>G	p.Asp586Glu	missense_variant	6/12	ENST00000640237.2	NP_001382979.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SCART1	ENST00000640237.2 linkuse as main transcript	c.1758C>G	p.Asp586Glu	missense_variant	6/12	5	NM_001396050.1	ENSP00000491516.1	Q4G0T1-1
SCART1	ENST00000463137.5 linkuse as main transcript	n.2521C>G		non_coding_transcript_exon_variant	6/11	2
SCART1	ENST00000482993.6 linkuse as main transcript	n.2903C>G		non_coding_transcript_exon_variant	5/10	2
SCART1	ENST00000488261.6 linkuse as main transcript	n.2669C>G		non_coding_transcript_exon_variant	4/14	2

Frequencies

GnomAD3 genomes

AF:

0.766

AC:

116464

AN:

151948

Hom.:

46895

Cov.:

show subpopulations

Gnomad AFR

AF:

0.485

Gnomad AMI

AF:

0.845

Gnomad AMR

AF:

0.765

Gnomad ASJ

AF:

0.899

Gnomad EAS

AF:

0.743

Gnomad SAS

AF:

0.908

Gnomad FIN

AF:

0.925

Gnomad MID

AF:

0.917

Gnomad NFE

AF:

0.895

Gnomad OTH

AF:

0.799

GnomAD3 exomes

AF:

0.834

AC:

15002

AN:

17986

Hom.:

6270

AF XY:

0.842

AC XY:

8263

AN XY:

9814

show subpopulations

Gnomad AFR exome

AF:

0.502

Gnomad AMR exome

AF:

0.732

Gnomad ASJ exome

AF:

0.889

Gnomad EAS exome

AF:

0.748

Gnomad SAS exome

AF:

0.901

Gnomad FIN exome

AF:

0.899

Gnomad NFE exome

AF:

0.880

Gnomad OTH exome

AF:

0.836

GnomAD4 exome

AF:

0.873

AC:

340553

AN:

390032

Hom.:

149320

Cov.:

AF XY:

0.878

AC XY:

181751

AN XY:

207108

show subpopulations

Gnomad4 AFR exome

AF:

0.498

Gnomad4 AMR exome

AF:

0.752

Gnomad4 ASJ exome

AF:

0.899

Gnomad4 EAS exome

AF:

0.728

Gnomad4 SAS exome

AF:

0.917

Gnomad4 FIN exome

AF:

0.911

Gnomad4 NFE exome

AF:

0.895

Gnomad4 OTH exome

AF:

0.854

GnomAD4 genome

AF:

0.766

AC:

116486

AN:

152058

Hom.:

46894

Cov.:

AF XY:

0.770

AC XY:

57206

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.485

Gnomad4 AMR

AF:

0.764

Gnomad4 ASJ

AF:

0.899

Gnomad4 EAS

AF:

0.742

Gnomad4 SAS

AF:

0.908

Gnomad4 FIN

AF:

0.925

Gnomad4 NFE

AF:

0.895

Gnomad4 OTH

AF:

0.802

Alfa

AF:

0.769

Hom.:

2930

TwinsUK

AF:

0.900

AC:

3339

ALSPAC

AF:

0.899

AC:

3466

ExAC

AF:

0.797

AC:

63943

Asia WGS

AF:

0.814

AC:

2817

AN:

3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.73

BayesDel_noAF

Benign

-0.44

CADD

Benign

DANN

Uncertain

1.0

Eigen

Benign

0.085

Eigen_PC

Benign

-0.037

FATHMM_MKL

Benign

0.30

LIST_S2

Benign

0.54

MetaRNN

Benign

0.0000011

MetaSVM

Benign

-1.1

MutPred

0.60

Gain of helix (P = 0.0425);

GERP RS

4.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

gMVP

0.20

Splicing

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