ENST00000791309.1:n.191A>G

Variant names:

• chr6-32668766-A-G
• rs9274666
• ENST00000791309.1:n.191A>G

Variant summary

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

The ENST00000791309.1(ENSG00000303029):​n.191A>G 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 0.574 in 147,760 control chromosomes in the GnomAD database, including 24,926 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 0.57 (24926 hom., cov: 27)
• Consequence: ENSG00000303029 ENST00000791309.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369
• Publications: 13 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791309.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303029	ENST00000791309.1		n.191A>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000303029	ENST00000791310.1		n.192A>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.574 AC: 84738 AN: 147638 Hom.: 24914 Cov.: 27

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.574 AC: 84784 AN: 147760 Hom.: 24926 Cov.: 27 AF XY: 0.568 AC XY: 40964 AN XY: 72128

African (AFR) AF: 0.594 AC: 23820 AN: 40074

American (AMR) AF: 0.511 AC: 7532 AN: 14744

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2142 AN: 3376

East Asian (EAS) AF: 0.583 AC: 2896 AN: 4968

South Asian (SAS) AF: 0.737 AC: 3451 AN: 4682

European-Finnish (FIN) AF: 0.463 AC: 4772 AN: 10298

Middle Eastern (MID) AF: 0.720 AC: 206 AN: 286

European-Non Finnish (NFE) AF: 0.576 AC: 38251 AN: 66388

Other (OTH) AF: 0.623 AC: 1279 AN: 2052

Alfa AF: 0.577 Hom.: 15669

Asia WGS AF: 0.714 AC: 2471 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.36
PhyloP100		-0.37
PromoterAI		0.025	Neutral

Splicing

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

Other links and lift over

dbSNP: rs9274666; hg19: chr6-32636543;