10-133468133-A-C

Variant names:

• chr10-133468133-A-C
• rs10776682
• NM_001396050.1:c.*165A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001396050.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCART1	NM_001396050.1	MANE Select	c.*165A>C		3_prime_UTR	Exon 12 of 12	NP_001382979.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCART1	ENST00000640237.2	TSL:5 MANE Select	c.*165A>C		3_prime_UTR	Exon 12 of 12	ENSP00000491516.1
	SCART1	ENST00000462252.1	TSL:2	n.2593A>C		non_coding_transcript_exon	Exon 3 of 3
	SCART1	ENST00000463137.5	TSL:2	n.3706A>C		non_coding_transcript_exon	Exon 11 of 11

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

African (AFR) AF: 0.673 AC: 7597 AN: 11282

American (AMR) AF: 0.367 AC: 5626 AN: 15332

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 3412 AN: 12018

East Asian (EAS) AF: 0.463 AC: 13055 AN: 28188

South Asian (SAS) AF: 0.306 AC: 9073 AN: 29628

European-Finnish (FIN) AF: 0.233 AC: 6219 AN: 26714

Middle Eastern (MID) AF: 0.334 AC: 925 AN: 2766

European-Non Finnish (NFE) AF: 0.270 AC: 59678 AN: 221080

Other (OTH) AF: 0.315 AC: 6988 AN: 22198

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

African (AFR) AF: 0.669 AC: 27745 AN: 41456

American (AMR) AF: 0.345 AC: 5268 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 965 AN: 3466

East Asian (EAS) AF: 0.440 AC: 2273 AN: 5164

South Asian (SAS) AF: 0.307 AC: 1482 AN: 4830

European-Finnish (FIN) AF: 0.204 AC: 2158 AN: 10576

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17989 AN: 67946

Other (OTH) AF: 0.367 AC: 775 AN: 2110

Alfa AF: 0.315 Hom.: 4808

Asia WGS AF: 0.373 AC: 1298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.61
PhyloP100		-1.6
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: rs10776682; hg19: chr10-135281637; COSMIC: COSV62987667;