chr6-52849339-C-A

Position:

• chr6-52849339-C-A

Variant summary

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

The ENST00000452866.1(GSTA11P):​n.415-289G>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 0.0459 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 ENST00000452866.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSTA11P	ENST00000452866.1	n.415-289G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.0221

Gnomad4 ASJ AF: 0.0262

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.0240

Gnomad4 FIN AF: 0.000847

Gnomad4 NFE AF: 0.00168

Gnomad4 OTH AF: 0.0359

Alfa AF: 0.0102 Hom.: 68

Bravo AF: 0.0528

Asia WGS AF: 0.0580 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7746993; hg19: chr6-52714137;