10-133508852-G-C

Variant names:

• chr10-133508852-G-C
• rs9418984
• ENST00000488261.6:n.4421+10847G>C

Variant summary

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

The ENST00000488261.6(SCART1):​n.4421+10847G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 151,978 control chromosomes in the GnomAD database, including 37,165 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 0.65 (37165 hom., cov: 33)
• Consequence: SCART1 ENST00000488261.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208
• 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]

LOC105378575 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378575	XR_007062396.1	n.6880+361C>G		intron_variant	Intron 4 of 4
LOC105378575	XR_946512.3	n.6859+361C>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCART1	ENST00000488261.6	n.4421+10847G>C		intron_variant	Intron 13 of 13	2

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99345 AN: 151858 Hom.: 37148 Cov.: 33

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.654 AC: 99370 AN: 151978 Hom.: 37165 Cov.: 33 AF XY: 0.653 AC XY: 48549 AN XY: 74298

African (AFR) AF: 0.263 AC: 10874 AN: 41358

American (AMR) AF: 0.690 AC: 10533 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2620 AN: 3470

East Asian (EAS) AF: 0.553 AC: 2855 AN: 5162

South Asian (SAS) AF: 0.610 AC: 2947 AN: 4828

European-Finnish (FIN) AF: 0.894 AC: 9467 AN: 10584

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.848 AC: 57656 AN: 67996

Other (OTH) AF: 0.675 AC: 1422 AN: 2108

Alfa AF: 0.721 Hom.: 4507

Asia WGS AF: 0.604 AC: 2096 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.9
DANN	Benign	0.77
PhyloP100		0.21
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: rs9418984; hg19: chr10-135322356;