1-17473923-A-G

Variant names:

• chr1-17473923-A-G
• rs6659366

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 0.952 in 151,924 control chromosomes in the GnomAD database, including 68,955 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 0.95 (68955 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.952 AC: 144491 AN: 151806 Hom.: 68894 Cov.: 29

Gnomad AFR AF: 0.982

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.979

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.945

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.948

Gnomad OTH AF: 0.958

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

GnomAD4 genome AF: 0.952 AC: 144611 AN: 151924 Hom.: 68955 Cov.: 29 AF XY: 0.949 AC XY: 70466 AN XY: 74242

African (AFR) AF: 0.982 AC: 40718 AN: 41472

American (AMR) AF: 0.959 AC: 14576 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.979 AC: 3399 AN: 3472

East Asian (EAS) AF: 0.780 AC: 4009 AN: 5138

South Asian (SAS) AF: 0.945 AC: 4557 AN: 4824

European-Finnish (FIN) AF: 0.918 AC: 9636 AN: 10494

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.949 AC: 64500 AN: 68002

Other (OTH) AF: 0.958 AC: 2021 AN: 2110

Alfa AF: 0.950 Hom.: 286115

Bravo AF: 0.953

Asia WGS AF: 0.882 AC: 3068 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.44
DANN	Benign	0.20
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs6659366; hg19: chr1-17800419;