1-17473923-A-G

Variant names:

• chr1-17473923-A-G
• rs6659366

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 0.952 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.952 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

Gnomad4 AFR AF: 0.982

Gnomad4 AMR AF: 0.959

Gnomad4 ASJ AF: 0.979

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.945

Gnomad4 FIN AF: 0.918

Gnomad4 NFE AF: 0.949

Gnomad4 OTH AF: 0.958

Alfa AF: 0.951 Hom.: 133686

Bravo AF: 0.953

Asia WGS AF: 0.882 AC: 3068 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6659366; hg19: chr1-17800419;