10-133508852-G-C

Variant summary

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

The XR_946512.3(LOC105378575):n.6859+361C>G variant causes a intron, non coding transcript 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: LOC105378575 XR_946512.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208

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=-0.82).
• 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/exons	MANE	UniProt
LOC105378575	XR_946512.3	n.6859+361C>G		intron_variant, non_coding_transcript_variant
LOC105378575	XR_007062396.1	n.6880+361C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCART1	ENST00000488261.6	n.4421+10847G>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.690

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.894

Gnomad4 NFE AF: 0.848

Gnomad4 OTH AF: 0.675

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9418984; hg19: chr10-135322356;