rs10776682

chr10-133468133-A-Cchr10-133468133-A-Gchr10-133468133-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001396050.1(SCART1):c.*165A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 521,234 control chromosomes in the GnomAD database, including 30,845 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 0.39 (13689 hom., cov: 34)
  • Exomes 𝑓: 0.30 (17156 hom.)
• Consequence: SCART1 NM_001396050.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCART1	NM_001396050.1	c.*165A>C		3_prime_UTR_variant	12/12	ENST00000640237.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCART1	ENST00000640237.2	c.*165A>C		3_prime_UTR_variant	12/12	5	NM_001396050.1	P1

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58958 AN: 151910 Hom.: 13649 Cov.: 34

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.372

GnomAD4 exome AF: 0.305 AC: 112573 AN: 369206 Hom.: 17156 Cov.: 0 AF XY: 0.302 AC XY: 58166 AN XY: 192572

Gnomad4 AFR exome AF: 0.673

Gnomad4 AMR exome AF: 0.367

Gnomad4 ASJ exome AF: 0.284

Gnomad4 EAS exome AF: 0.463

Gnomad4 SAS exome AF: 0.306

Gnomad4 FIN exome AF: 0.233

Gnomad4 NFE exome AF: 0.270

Gnomad4 OTH exome AF: 0.315

GnomAD4 genome AF: 0.388 AC: 59038 AN: 152028 Hom.: 13689 Cov.: 34 AF XY: 0.384 AC XY: 28507 AN XY: 74324

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.367

Alfa AF: 0.309 Hom.: 2985

Asia WGS AF: 0.373 AC: 1298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.77
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10776682; hg19: chr10-135281637; COSMIC: COSV62987667;