rs4715359

Variant names:

• chr6-52876817-G-A
• rs4715359

Your query was ambiguous. Multiple possible variants found:

• chr6-52876817-G-A
• chr6-52876817-G-C
• chr6-52876817-G-T

Variant summary

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

The variant allele was found at a frequency of 0.676 in 152,462 control chromosomes in the GnomAD database, including 35,047 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 0.68 (34968 hom., cov: 32)
  • Exomes 𝑓: 0.66 (79 hom.)
• Consequence: GSTA10P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• Publications: 4 publications found

Genes affected

GSTA10P (HGNC:49904): (glutathione S-transferase alpha 10, pseudogene)

ENSG00000309879 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSTA10P		n.52876817G>A		intragenic_variant
LOC105375091	XR_001744165.2	n.520+5305G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTA10P	ENST00000412182.2	n.437+95C>T		intron_variant	Intron 4 of 5	6
ENSG00000309879	ENST00000844911.1	n.266+216C>T		intron_variant	Intron 3 of 3
ENSG00000309879	ENST00000844912.1	n.393+216C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102800 AN: 151966 Hom.: 34941 Cov.: 32

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.651

GnomAD4 exome AF: 0.661 AC: 250 AN: 378 Hom.: 79 AF XY: 0.650 AC XY: 147 AN XY: 226

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.661 AC: 242 AN: 366

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.667 AC: 4 AN: 6

Other (OTH) AF: 0.667 AC: 4 AN: 6

GnomAD4 genome AF: 0.676 AC: 102878 AN: 152084 Hom.: 34968 Cov.: 32 AF XY: 0.680 AC XY: 50544 AN XY: 74348

African (AFR) AF: 0.707 AC: 29321 AN: 41486

American (AMR) AF: 0.700 AC: 10696 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1938 AN: 3462

East Asian (EAS) AF: 0.845 AC: 4372 AN: 5172

South Asian (SAS) AF: 0.736 AC: 3540 AN: 4812

European-Finnish (FIN) AF: 0.660 AC: 6988 AN: 10592

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43839 AN: 67968

Other (OTH) AF: 0.655 AC: 1380 AN: 2108

Alfa AF: 0.645 Hom.: 53221

Bravo AF: 0.681

Asia WGS AF: 0.764 AC: 2658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.54
PhyloP100		0.062

Splicing

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

Other links and lift over

dbSNP: rs4715359; hg19: chr6-52741615;