6-69467024-A-G

Variant names:

• chr6-69467024-A-G
• rs2094596

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 0.911 in 152,246 control chromosomes in the GnomAD database, including 63,188 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 0.91 (63188 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 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: 0.911 AC: 138542 AN: 152128 Hom.: 63142 Cov.: 33

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.935

Gnomad ASJ AF: 0.936

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.911 AC: 138648 AN: 152246 Hom.: 63188 Cov.: 33 AF XY: 0.913 AC XY: 67915 AN XY: 74420

Gnomad4 AFR AF: 0.892

Gnomad4 AMR AF: 0.935

Gnomad4 ASJ AF: 0.936

Gnomad4 EAS AF: 0.964

Gnomad4 SAS AF: 0.894

Gnomad4 FIN AF: 0.926

Gnomad4 NFE AF: 0.911

Gnomad4 OTH AF: 0.910

Alfa AF: 0.909 Hom.: 81045

Bravo AF: 0.911

Asia WGS AF: 0.939 AC: 3268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2094596; hg19: chr6-70176916;