rs474939

chr1-182569480-A-G

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 0.895 in 151,952 control chromosomes in the GnomAD database, including 61,323 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 0.89 (61323 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

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 (NFE) allele frequency at 95% confidence interval = 0.914 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: 0.895 AC: 135892 AN: 151836 Hom.: 61290 Cov.: 28

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.892

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.895 AC: 135978 AN: 151952 Hom.: 61323 Cov.: 28 AF XY: 0.893 AC XY: 66340 AN XY: 74260

Gnomad4 AFR AF: 0.904

Gnomad4 AMR AF: 0.857

Gnomad4 ASJ AF: 0.893

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.903

Gnomad4 FIN AF: 0.941

Gnomad4 NFE AF: 0.921

Gnomad4 OTH AF: 0.889

Alfa AF: 0.903 Hom.: 49833

Bravo AF: 0.882

Asia WGS AF: 0.756 AC: 2631 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	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs474939; hg19: chr1-182538615;