chr10-133519299-G-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000488261.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCART1	ENST00000488261.6	TSL:2	n.4422-3972G>A		intron	N/A
	ENSG00000278518	ENST00000822676.1		n.231-4971C>T		intron	N/A
	ENSG00000278518	ENST00000822677.1		n.65+4311C>T		intron	N/A

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 v4.9

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;