10-133461854-T-G

Variant names:

• chr10-133461854-T-G
• rs2252728
• NM_001396050.1:c.1969+1684T>G

Variant summary

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

The NM_001396050.1(SCART1):​c.1969+1684T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,166 control chromosomes in the GnomAD database, including 53,516 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 0.84 (53516 hom., cov: 34)
• Consequence: SCART1 NM_001396050.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918
• Publications: 2 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 (SAS) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCART1	NM_001396050.1	c.1969+1684T>G		intron_variant	Intron 6 of 11	ENST00000640237.2	NP_001382979.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCART1	ENST00000640237.2	c.1969+1684T>G		intron_variant	Intron 6 of 11	5	NM_001396050.1	ENSP00000491516.1
SCART1	ENST00000463137.5	n.2732+1684T>G		intron_variant	Intron 6 of 10	2
SCART1	ENST00000482993.6	n.3114+1684T>G		intron_variant	Intron 5 of 9	2
SCART1	ENST00000488261.6	n.2880+1684T>G		intron_variant	Intron 4 of 13	2

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127136 AN: 152048 Hom.: 53480 Cov.: 34

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.836 AC: 127225 AN: 152166 Hom.: 53516 Cov.: 34 AF XY: 0.836 AC XY: 62220 AN XY: 74382

African (AFR) AF: 0.756 AC: 31353 AN: 41462

American (AMR) AF: 0.799 AC: 12210 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3117 AN: 3468

East Asian (EAS) AF: 0.742 AC: 3845 AN: 5180

South Asian (SAS) AF: 0.903 AC: 4352 AN: 4820

European-Finnish (FIN) AF: 0.894 AC: 9477 AN: 10602

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.883 AC: 60094 AN: 68026

Other (OTH) AF: 0.859 AC: 1816 AN: 2114

Alfa AF: 0.877 Hom.: 25355

Bravo AF: 0.825

Asia WGS AF: 0.830 AC: 2888 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	2.5
DANN	Benign	0.24
PhyloP100		-0.92
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: rs2252728; hg19: chr10-135275358;