6-32607592-G-T

Variant names:

• chr6-32607592-G-T
• rs9271055

Variant summary

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

The variant allele was found at a frequency of 0.845 in 151,006 control chromosomes in the GnomAD database, including 53,923 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 0.84 (53923 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.745
• Publications: 46 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.845 AC: 127446 AN: 150892 Hom.: 53880 Cov.: 26

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.900

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.845 AC: 127539 AN: 151006 Hom.: 53923 Cov.: 26 AF XY: 0.843 AC XY: 62142 AN XY: 73690

African (AFR) AF: 0.837 AC: 34338 AN: 41024

American (AMR) AF: 0.881 AC: 13399 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 3176 AN: 3462

East Asian (EAS) AF: 0.820 AC: 4186 AN: 5104

South Asian (SAS) AF: 0.765 AC: 3638 AN: 4754

European-Finnish (FIN) AF: 0.858 AC: 8934 AN: 10414

Middle Eastern (MID) AF: 0.896 AC: 258 AN: 288

European-Non Finnish (NFE) AF: 0.841 AC: 56962 AN: 67746

Other (OTH) AF: 0.869 AC: 1821 AN: 2096

Alfa AF: 0.843 Hom.: 66604

Bravo AF: 0.850

Asia WGS AF: 0.746 AC: 2597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	10
DANN	Benign	0.56
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs9271055; hg19: chr6-32575369;