chr6-32669089-A-T

Variant names:

• chr6-32669089-A-T
• rs3134996
• ENST00000791309.1:n.423A>T

Variant summary

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

The ENST00000791309.1(ENSG00000303029):​n.423A>T 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 0.631 in 151,384 control chromosomes in the GnomAD database, including 30,560 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 0.63 (30560 hom., cov: 29)
• Consequence: ENSG00000303029 ENST00000791309.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 29 publications found

Genes affected

ENSG00000303029 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 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
ENSG00000303029	ENST00000791309.1	n.423A>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000303029	ENST00000791310.1	n.515A>T		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95425 AN: 151266 Hom.: 30550 Cov.: 29

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.817

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.631 AC: 95482 AN: 151384 Hom.: 30560 Cov.: 29 AF XY: 0.630 AC XY: 46590 AN XY: 73930

African (AFR) AF: 0.564 AC: 23271 AN: 41270

American (AMR) AF: 0.696 AC: 10575 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2449 AN: 3452

East Asian (EAS) AF: 0.858 AC: 4400 AN: 5126

South Asian (SAS) AF: 0.789 AC: 3791 AN: 4806

European-Finnish (FIN) AF: 0.540 AC: 5651 AN: 10474

Middle Eastern (MID) AF: 0.810 AC: 235 AN: 290

European-Non Finnish (NFE) AF: 0.637 AC: 43170 AN: 67776

Other (OTH) AF: 0.660 AC: 1384 AN: 2098

Alfa AF: 0.660 Hom.: 17436

Bravo AF: 0.642

Asia WGS AF: 0.783 AC: 2720 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	1.6
DANN	Benign	0.53
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs3134996; hg19: chr6-32636866;