chr6-122905432-C-T

Variant names:

• chr6-122905432-C-T
• rs9398707

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 0.808 in 152,200 control chromosomes in the GnomAD database, including 50,012 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 0.81 (50012 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.887 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: 0.809 AC: 122961 AN: 152082 Hom.: 49985 Cov.: 33

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.862

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.904

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.808 AC: 123042 AN: 152200 Hom.: 50012 Cov.: 33 AF XY: 0.808 AC XY: 60101 AN XY: 74428

African (AFR) AF: 0.725 AC: 30089 AN: 41518

American (AMR) AF: 0.874 AC: 13371 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.862 AC: 2992 AN: 3472

East Asian (EAS) AF: 0.909 AC: 4709 AN: 5182

South Asian (SAS) AF: 0.792 AC: 3824 AN: 4826

European-Finnish (FIN) AF: 0.780 AC: 8270 AN: 10598

Middle Eastern (MID) AF: 0.911 AC: 266 AN: 292

European-Non Finnish (NFE) AF: 0.839 AC: 57028 AN: 67992

Other (OTH) AF: 0.827 AC: 1749 AN: 2114

Alfa AF: 0.833 Hom.: 152526

Bravo AF: 0.815

Asia WGS AF: 0.860 AC: 2988 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.27
DANN	Benign	0.73
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs9398707; hg19: chr6-123226577;