6-122905432-C-T

Position:

• chr6-122905432-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;