rs577317

chr1-166661797-A-Gchr1-166661797-A-T

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 0.912 in 152,192 control chromosomes in the GnomAD database, including 63,364 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 (63364 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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 = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.912 AC: 138718 AN: 152074 Hom.: 63316 Cov.: 31

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.910

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.912 AC: 138825 AN: 152192 Hom.: 63364 Cov.: 31 AF XY: 0.913 AC XY: 67940 AN XY: 74418

Gnomad4 AFR AF: 0.888

Gnomad4 AMR AF: 0.931

Gnomad4 ASJ AF: 0.942

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.969

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.910

Gnomad4 OTH AF: 0.922

Alfa AF: 0.907 Hom.: 8479

Bravo AF: 0.913

Asia WGS AF: 0.974 AC: 3388 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	0.041
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs577317; hg19: chr1-166631034;