chr10-133468133-A-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001396050.1(SCART1):​c.*165A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000027 in 370,346 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 34)
  • Exomes 𝑓: 0.0000027 (0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

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>G		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>G		3_prime_UTR	Exon 12 of 12	ENSP00000491516.1
	SCART1	ENST00000462252.1	TSL:2	n.2593A>G		non_coding_transcript_exon	Exon 3 of 3
	SCART1	ENST00000463137.5	TSL:2	n.3706A>G		non_coding_transcript_exon	Exon 11 of 11

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 0.00000270 AC: 1 AN: 370346 Hom.: 0 Cov.: 0 AF XY: 0.00000518 AC XY: 1 AN XY: 193142

African (AFR) AF: 0.00 AC: 0 AN: 11314

American (AMR) AF: 0.00 AC: 0 AN: 15402

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12050

East Asian (EAS) AF: 0.00 AC: 0 AN: 28236

South Asian (SAS) AF: 0.00 AC: 0 AN: 29740

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26788

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2778

European-Non Finnish (NFE) AF: 0.00000451 AC: 1 AN: 221774

Other (OTH) AF: 0.00 AC: 0 AN: 22264

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.79
DANN	Benign	0.64
PhyloP100		-1.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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;