rs1536827

Variant names:

• chr10-133492654-C-T
• rs1536827
• XR_007062396.1:n.7068G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.939 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCART1	ENST00000488261.6	TSL:2	n.4041-633C>T		intron	N/A

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

African (AFR) AF: 0.641 AC: 26523 AN: 41400

American (AMR) AF: 0.840 AC: 12829 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3088 AN: 3470

East Asian (EAS) AF: 0.802 AC: 4154 AN: 5182

South Asian (SAS) AF: 0.962 AC: 4641 AN: 4826

European-Finnish (FIN) AF: 0.941 AC: 9984 AN: 10610

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.931 AC: 63337 AN: 68002

Other (OTH) AF: 0.857 AC: 1809 AN: 2112

Alfa AF: 0.890 Hom.: 143978

Asia WGS AF: 0.904 AC: 3140 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.75
PhyloP100		-1.0
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: rs1536827; hg19: chr10-135306158;