rs4838767

Variant names:

• chr10-133520114-C-A
• rs4838767
• XR_007062396.1:n.6251G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The XR_007062396.1(LOC105378575):​n.6251G>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_007062396.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCART1	ENST00000488261.6	TSL:2	n.4422-3157C>A		intron	N/A
	ENSG00000278518	ENST00000822676.1		n.231-5786G>T		intron	N/A
	ENSG00000278518	ENST00000822677.1		n.65+3496G>T		intron	N/A

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

African (AFR) AF: 0.856 AC: 35509 AN: 41502

American (AMR) AF: 0.928 AC: 14206 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3382 AN: 3472

East Asian (EAS) AF: 0.827 AC: 4292 AN: 5190

South Asian (SAS) AF: 0.921 AC: 4445 AN: 4826

European-Finnish (FIN) AF: 0.984 AC: 10460 AN: 10628

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.989 AC: 67310 AN: 68036

Other (OTH) AF: 0.946 AC: 2001 AN: 2116

Alfa AF: 0.950 Hom.: 10158

Bravo AF: 0.931

Asia WGS AF: 0.871 AC: 3031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.48
PhyloP100		-0.21
PromoterAI		-0.0026	Neutral
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: rs4838767; hg19: chr10-135333618;