chr6-35436660-G-A

Variant names:

• chr6-35436660-G-A
• rs9462085
• ENST00000794874.1:n.-13G>A

Variant summary

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

The ENST00000794874.1(ENSG00000303476):​n.-13G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 152,060 control chromosomes in the GnomAD database, including 29,381 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 0.60 (29381 hom., cov: 32)
• Consequence: ENSG00000303476 ENST00000794874.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38
• Publications: 22 publications found

Genes affected

ENSG00000303476 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794874.1. 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
	ENSG00000303476	ENST00000794874.1		n.-13G>A		upstream_gene	N/A
	ENSG00000303476	ENST00000794875.1		n.-30G>A		upstream_gene	N/A
	ENSG00000303476	ENST00000794876.1		n.-30G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90952 AN: 151942 Hom.: 29356 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.598 AC: 90995 AN: 152060 Hom.: 29381 Cov.: 32 AF XY: 0.602 AC XY: 44773 AN XY: 74328

African (AFR) AF: 0.358 AC: 14835 AN: 41450

American (AMR) AF: 0.650 AC: 9933 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1627 AN: 3470

East Asian (EAS) AF: 0.450 AC: 2315 AN: 5148

South Asian (SAS) AF: 0.662 AC: 3199 AN: 4830

European-Finnish (FIN) AF: 0.821 AC: 8701 AN: 10592

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.713 AC: 48439 AN: 67972

Other (OTH) AF: 0.568 AC: 1197 AN: 2108

Alfa AF: 0.672 Hom.: 53504

Bravo AF: 0.572

Asia WGS AF: 0.517 AC: 1797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	13
DANN	Benign	0.58
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs9462085; hg19: chr6-35404437;