6-52957739-C-T

Variant names:

• chr6-52957739-C-T
• rs521664
• ENST00000448991.6:n.44-1261G>A

Variant summary

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

The ENST00000448991.6(ENSG00000291036):​n.44-1261G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 152,066 control chromosomes in the GnomAD database, including 34,706 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 0.66 (34706 hom., cov: 32)
• Consequence: ENSG00000291036 ENST00000448991.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

Genes affected

ENSG00000291036 (HGNC:):

GSTA9P (HGNC:49902): (glutathione S-transferase alpha 9, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291036	ENST00000448991.6	n.44-1261G>A		intron_variant	Intron 1 of 5	3
GSTA9P	ENST00000406231.1	n.-218G>A		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100431 AN: 151948 Hom.: 34672 Cov.: 32

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.661 AC: 100502 AN: 152066 Hom.: 34706 Cov.: 32 AF XY: 0.653 AC XY: 48497 AN XY: 74324

Gnomad4 AFR AF: 0.859

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.625

Alfa AF: 0.606 Hom.: 55259

Bravo AF: 0.660

Asia WGS AF: 0.485 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.20
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs521664; hg19: chr6-52822537;