rs4715359

chr6-52876817-G-Achr6-52876817-G-Cchr6-52876817-G-T

Variant summary

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

The ENST00000412182.2(GSTA10P):n.437+95C>T 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 0.676 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 ENST00000412182.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620

Genes affected

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

LOC105375091 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105375091	XR_001744165.2	n.520+5305G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSTA10P	ENST00000412182.2	n.437+95C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 FIN exome AF: 0.661

Gnomad4 NFE exome AF: 0.667

Gnomad4 OTH exome AF: 0.667

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

Gnomad4 AFR AF: 0.707

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.845

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.655

Alfa AF: 0.642 Hom.: 41524

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4715359; hg19: chr6-52741615;