chr6-52849339-C-A

Variant names:

• chr6-52849339-C-A
• rs7746993

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 0.0459 in 152,272 control chromosomes in the GnomAD database, including 452 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 0.046 (452 hom., cov: 32)
• Consequence: GSTA11P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37
• Publications: 6 publications found

Genes affected

GSTA11P (HGNC:49905): (glutathione S-transferase alpha 11, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000452866.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTA11P	ENST00000452866.1	TSL:6	n.415-289G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0460 AC: 6994 AN: 152154 Hom.: 453 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0221

Gnomad ASJ AF: 0.0262

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0244

Gnomad FIN AF: 0.000847

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00168

Gnomad OTH AF: 0.0368

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

GnomAD4 genome AF: 0.0459 AC: 6995 AN: 152272 Hom.: 452 Cov.: 32 AF XY: 0.0455 AC XY: 3384 AN XY: 74452

African (AFR) AF: 0.135 AC: 5588 AN: 41530

American (AMR) AF: 0.0221 AC: 338 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0262 AC: 91 AN: 3470

East Asian (EAS) AF: 0.128 AC: 660 AN: 5156

South Asian (SAS) AF: 0.0240 AC: 116 AN: 4830

European-Finnish (FIN) AF: 0.000847 AC: 9 AN: 10624

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00168 AC: 114 AN: 68030

Other (OTH) AF: 0.0359 AC: 76 AN: 2116

Alfa AF: 0.0185 Hom.: 432

Bravo AF: 0.0528

Asia WGS AF: 0.0580 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.37
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs7746993; hg19: chr6-52714137;