6-69467024-A-G

Variant names:

• chr6-69467024-A-G
• rs2094596

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 0.911 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.892 AC: 37061 AN: 41560

American (AMR) AF: 0.935 AC: 14309 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.936 AC: 3249 AN: 3472

East Asian (EAS) AF: 0.964 AC: 4958 AN: 5144

South Asian (SAS) AF: 0.894 AC: 4313 AN: 4826

European-Finnish (FIN) AF: 0.926 AC: 9833 AN: 10614

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.911 AC: 61960 AN: 68006

Other (OTH) AF: 0.910 AC: 1922 AN: 2112

Alfa AF: 0.910 Hom.: 103789

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2094596; hg19: chr6-70176916;