6-32598077-C-T

Variant names:

• chr6-32598077-C-T
• rs9270650

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 0.745 in 151,314 control chromosomes in the GnomAD database, including 42,197 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 0.74 (42197 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.745 AC: 112637 AN: 151196 Hom.: 42162 Cov.: 28

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.745 AC: 112723 AN: 151314 Hom.: 42197 Cov.: 28 AF XY: 0.742 AC XY: 54840 AN XY: 73888

African (AFR) AF: 0.768 AC: 31603 AN: 41166

American (AMR) AF: 0.788 AC: 11955 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2722 AN: 3456

East Asian (EAS) AF: 0.804 AC: 4146 AN: 5158

South Asian (SAS) AF: 0.727 AC: 3478 AN: 4786

European-Finnish (FIN) AF: 0.657 AC: 6859 AN: 10436

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.729 AC: 49472 AN: 67834

Other (OTH) AF: 0.770 AC: 1616 AN: 2100

Alfa AF: 0.745 Hom.: 20780

Bravo AF: 0.759

Asia WGS AF: 0.710 AC: 2473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
DANN	Benign	0.13
PhyloP100		-0.078

Splicing

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

Other links and lift over

dbSNP: rs9270650; hg19: chr6-32565854;