10-133463341-A-G

Variant names:

• chr10-133463341-A-G
• rs2255518
• NM_001396050.1:c.1970-1265A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001396050.1(SCART1):​c.1970-1265A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 151,844 control chromosomes in the GnomAD database, including 33,896 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 0.64 (33896 hom., cov: 31)
• Consequence: SCART1 NM_001396050.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.541
• Publications: 6 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCART1	NM_001396050.1	c.1970-1265A>G		intron_variant	Intron 6 of 11	ENST00000640237.2	NP_001382979.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCART1	ENST00000640237.2	c.1970-1265A>G		intron_variant	Intron 6 of 11	5	NM_001396050.1	ENSP00000491516.1
SCART1	ENST00000463137.5	n.2733-1765A>G		intron_variant	Intron 6 of 10	2
SCART1	ENST00000482993.6	n.3115-1265A>G		intron_variant	Intron 5 of 9	2
SCART1	ENST00000488261.6	n.2881-1265A>G		intron_variant	Intron 4 of 13	2

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97332 AN: 151728 Hom.: 33882 Cov.: 31

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.667

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.641 AC: 97367 AN: 151844 Hom.: 33896 Cov.: 31 AF XY: 0.644 AC XY: 47815 AN XY: 74212

African (AFR) AF: 0.342 AC: 14152 AN: 41320

American (AMR) AF: 0.649 AC: 9901 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2735 AN: 3472

East Asian (EAS) AF: 0.562 AC: 2889 AN: 5142

South Asian (SAS) AF: 0.701 AC: 3374 AN: 4812

European-Finnish (FIN) AF: 0.832 AC: 8799 AN: 10574

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.784 AC: 53287 AN: 67948

Other (OTH) AF: 0.671 AC: 1413 AN: 2106

Alfa AF: 0.733 Hom.: 157144

Asia WGS AF: 0.631 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.65
PhyloP100		0.54
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2255518; hg19: chr10-135276845;