rs4838767

Positions:

• chr10-133520114-C-A
• chr10-133520114-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_946512.3(LOC105378575):​n.6230G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.938 in 152,280 control chromosomes in the GnomAD database, including 67,216 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 0.94 (67216 hom., cov: 35)
• Consequence: LOC105378575 XR_946512.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

Genes affected

LOC105378575 (HGNC:):

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378575	XR_946512.3	n.6230G>T		non_coding_transcript_exon_variant	2/5
LOC105378575	XR_007062396.1	n.6251G>T		non_coding_transcript_exon_variant	2/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCART1	ENST00000488261.6	n.4422-3157C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.938 AC: 142685 AN: 152162 Hom.: 67163 Cov.: 35

Gnomad AFR AF: 0.856

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.984

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.989

Gnomad OTH AF: 0.945

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

GnomAD4 genome AF: 0.938 AC: 142798 AN: 152280 Hom.: 67216 Cov.: 35 AF XY: 0.936 AC XY: 69709 AN XY: 74464

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.928

Gnomad4 ASJ AF: 0.974

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.921

Gnomad4 FIN AF: 0.984

Gnomad4 NFE AF: 0.989

Gnomad4 OTH AF: 0.946

Alfa AF: 0.952 Hom.: 9869

Bravo AF: 0.931

Asia WGS AF: 0.871 AC: 3031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.48

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4838767; hg19: chr10-135333618;