rs1536827

chr10-133492654-C-T

Variant summary

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

The XR_946512.3(LOC105378575):n.7047G>A 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 0.838 in 152,080 control chromosomes in the GnomAD database, including 54,423 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 (54423 hom., cov: 33)
• Consequence: LOC105378575 XR_946512.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378575	XR_946512.3	n.7047G>A		non_coding_transcript_exon_variant	5/5
LOC105378575	XR_007062396.1	n.7068G>A		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCART1	ENST00000488261.6	n.4041-633C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127420 AN: 151962 Hom.: 54397 Cov.: 33

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.838 AC: 127496 AN: 152080 Hom.: 54423 Cov.: 33 AF XY: 0.839 AC XY: 62419 AN XY: 74356

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.840

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.962

Gnomad4 FIN AF: 0.941

Gnomad4 NFE AF: 0.931

Gnomad4 OTH AF: 0.857

Alfa AF: 0.912 Hom.: 107024

Asia WGS AF: 0.904 AC: 3140 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.8
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1536827; hg19: chr10-135306158;