6-122905432-C-T

Variant names:

• chr6-122905432-C-T
• rs9398707

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.874

Gnomad4 ASJ AF: 0.862

Gnomad4 EAS AF: 0.909

Gnomad4 SAS AF: 0.792

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.827

Alfa AF: 0.838 Hom.: 69907

Bravo AF: 0.815

Asia WGS AF: 0.860 AC: 2988 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9398707; hg19: chr6-123226577;