6-32669153-T-C

Variant names:

• chr6-32669153-T-C
• rs9274689
• ENST00000791309.1:n.*1T>C

Variant summary

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

The ENST00000791309.1(ENSG00000303029):​n.*1T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,234 control chromosomes in the GnomAD database, including 18,128 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 0.48 (18128 hom., cov: 30)
• Consequence: ENSG00000303029 ENST00000791309.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863
• Publications: 11 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 (EAS) allele frequency at 95% confidence interval = 0.669 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

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
	ENSG00000303029	ENST00000791309.1		n.*1T>C		downstream_gene	N/A
	ENSG00000303029	ENST00000791310.1		n.*4T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73100 AN: 151116 Hom.: 18119 Cov.: 30

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.613

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.484 AC: 73147 AN: 151234 Hom.: 18128 Cov.: 30 AF XY: 0.486 AC XY: 35855 AN XY: 73850

African (AFR) AF: 0.439 AC: 18107 AN: 41240

American (AMR) AF: 0.595 AC: 9029 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2128 AN: 3462

East Asian (EAS) AF: 0.688 AC: 3527 AN: 5126

South Asian (SAS) AF: 0.542 AC: 2596 AN: 4794

European-Finnish (FIN) AF: 0.428 AC: 4468 AN: 10450

Middle Eastern (MID) AF: 0.601 AC: 173 AN: 288

European-Non Finnish (NFE) AF: 0.466 AC: 31573 AN: 67712

Other (OTH) AF: 0.510 AC: 1070 AN: 2100

Alfa AF: 0.478 Hom.: 3935

Bravo AF: 0.501

Asia WGS AF: 0.544 AC: 1889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.87
PhyloP100		-0.86

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: rs9274689;

hg19: chr6-32636930;