6-32623122-G-T

Variant names:

• chr6-32623122-G-T
• rs9271586
• ENST00000843606.1:n.2C>A

Variant summary

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

The ENST00000843606.1(ENSG00000309733):​n.2C>A 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 0.435 in 151,848 control chromosomes in the GnomAD database, including 14,756 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 0.43 (14756 hom., cov: 32)
• Consequence: ENSG00000309733 ENST00000843606.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468
• Publications: 14 publications found

Genes affected

ENSG00000309733 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843606.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309733	ENST00000843606.1		n.2C>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 65986 AN: 151730 Hom.: 14741 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.391

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.435 AC: 66043 AN: 151848 Hom.: 14756 Cov.: 32 AF XY: 0.434 AC XY: 32186 AN XY: 74214

African (AFR) AF: 0.360 AC: 14889 AN: 41404

American (AMR) AF: 0.471 AC: 7183 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1742 AN: 3468

East Asian (EAS) AF: 0.448 AC: 2316 AN: 5168

South Asian (SAS) AF: 0.418 AC: 2016 AN: 4818

European-Finnish (FIN) AF: 0.461 AC: 4854 AN: 10520

Middle Eastern (MID) AF: 0.372 AC: 108 AN: 290

European-Non Finnish (NFE) AF: 0.462 AC: 31375 AN: 67906

Other (OTH) AF: 0.450 AC: 949 AN: 2108

Alfa AF: 0.439 Hom.: 6699

Bravo AF: 0.439

Asia WGS AF: 0.395 AC: 1379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.2
DANN	Benign	0.43
PhyloP100		-0.47

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9271586;

hg19: chr6-32590899;