rs4659007

chr1-119503863-T-Achr1-119503863-T-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 0.749 in 151,910 control chromosomes in the GnomAD database, including 43,467 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 0.75 (43467 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 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: 0.749 AC: 113683 AN: 151790 Hom.: 43422 Cov.: 30

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.663

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.749 AC: 113787 AN: 151910 Hom.: 43467 Cov.: 30 AF XY: 0.757 AC XY: 56192 AN XY: 74212

Gnomad4 AFR AF: 0.879

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.718

Alfa AF: 0.602 Hom.: 1682

Bravo AF: 0.757

Asia WGS AF: 0.865 AC: 3009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.60
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4659007; hg19: chr1-120046486; COSMIC: COSV52489902;