ENST00000488261.6:n.4422-3972G>A

Variant names:

• chr10-133519299-G-A
• rs10857733
• ENST00000488261.6:n.4422-3972G>A

Variant summary

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

The ENST00000488261.6(SCART1):​n.4422-3972G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 151,998 control chromosomes in the GnomAD database, including 1,211 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 0.11 (1211 hom., cov: 34)
• Consequence: SCART1 ENST00000488261.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• 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]

ENSG00000278518 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378575	XR_007062396.1	n.6694+372C>T		intron_variant	Intron 2 of 4
LOC105378575	XR_946512.3	n.6673+372C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCART1	ENST00000488261.6	n.4422-3972G>A		intron_variant	Intron 13 of 13	2
ENSG00000278518	ENST00000822676.1	n.231-4971C>T		intron_variant	Intron 1 of 2
ENSG00000278518	ENST00000822677.1	n.65+4311C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16405 AN: 151878 Hom.: 1202 Cov.: 34

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0848

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.0269

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0494

Gnomad OTH AF: 0.0943

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

GnomAD4 genome AF: 0.108 AC: 16446 AN: 151998 Hom.: 1211 Cov.: 34 AF XY: 0.107 AC XY: 7980 AN XY: 74304

African (AFR) AF: 0.222 AC: 9198 AN: 41414

American (AMR) AF: 0.126 AC: 1917 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0848 AC: 294 AN: 3468

East Asian (EAS) AF: 0.203 AC: 1049 AN: 5174

South Asian (SAS) AF: 0.0174 AC: 84 AN: 4818

European-Finnish (FIN) AF: 0.0269 AC: 285 AN: 10584

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0494 AC: 3360 AN: 67950

Other (OTH) AF: 0.0938 AC: 198 AN: 2112

Alfa AF: 0.0750 Hom.: 1549

Asia WGS AF: 0.0860 AC: 300 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	1.5
DANN	Benign	0.40
PhyloP100		0.16
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: rs10857733; hg19: chr10-135332803;