chr6-52744866-C-T

Variant names:

• chr6-52744866-C-T
• rs2608615
• NR_033760.1:n.294G>A

Variant summary

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

The NR_033760.1(GSTA7P):​n.294G>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 0.171 in 152,088 control chromosomes in the GnomAD database, including 3,764 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 0.17 (3764 hom., cov: 32)
• Consequence: GSTA7P NR_033760.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626
• Publications: 4 publications found

Genes affected

GSTA7P (HGNC:4631): (glutathione S-transferase alpha 7, pseudogene)

ENSG00000301411 (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 (AFR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_033760.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTA7P	NR_033760.1		n.294G>A		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301411	ENST00000778749.1		n.171-210G>A		intron	N/A
	ENSG00000301411	ENST00000778750.1		n.171-210G>A		intron	N/A
	GSTA7P	ENST00000438425.1	TSL:6	n.-210G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25994 AN: 151970 Hom.: 3752 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.0777

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0805

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.171 AC: 26050 AN: 152088 Hom.: 3764 Cov.: 32 AF XY: 0.169 AC XY: 12531 AN XY: 74338

African (AFR) AF: 0.392 AC: 16258 AN: 41428

American (AMR) AF: 0.107 AC: 1629 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3468

East Asian (EAS) AF: 0.135 AC: 701 AN: 5176

South Asian (SAS) AF: 0.0777 AC: 375 AN: 4824

European-Finnish (FIN) AF: 0.0686 AC: 726 AN: 10586

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0805 AC: 5473 AN: 68010

Other (OTH) AF: 0.151 AC: 319 AN: 2110

Alfa AF: 0.113 Hom.: 2092

Bravo AF: 0.185

Asia WGS AF: 0.111 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.55
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2608615; hg19: chr6-52609664;