6-15669255-A-G

Variant names:

• chr6-15669255-A-G
• rs885773

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 0.99 in 152,280 control chromosomes in the GnomAD database, including 74,654 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 0.99 (74654 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.990 AC: 150665 AN: 152162 Hom.: 74594 Cov.: 31

Gnomad AFR AF: 0.997

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.992

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.992

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

GnomAD4 genome AF: 0.990 AC: 150784 AN: 152280 Hom.: 74654 Cov.: 31 AF XY: 0.991 AC XY: 73771 AN XY: 74458

African (AFR) AF: 0.997 AC: 41426 AN: 41546

American (AMR) AF: 0.992 AC: 15179 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.995 AC: 3456 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5176 AN: 5176

South Asian (SAS) AF: 0.999 AC: 4819 AN: 4822

European-Finnish (FIN) AF: 0.978 AC: 10390 AN: 10622

Middle Eastern (MID) AF: 0.997 AC: 293 AN: 294

European-Non Finnish (NFE) AF: 0.985 AC: 67040 AN: 68030

Other (OTH) AF: 0.992 AC: 2094 AN: 2110

Alfa AF: 0.990 Hom.: 9398

Bravo AF: 0.991

Asia WGS AF: 1.00 AC: 3477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.65
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs885773; hg19: chr6-15669486;