rs1479924

Variant names:

• chr4-122466445-G-A
• rs1479924

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 0.758 in 152,192 control chromosomes in the GnomAD database, including 43,902 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 0.76 (43902 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.841 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: 0.758 AC: 115260 AN: 152074 Hom.: 43863 Cov.: 33

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.758 AC: 115356 AN: 152192 Hom.: 43902 Cov.: 33 AF XY: 0.768 AC XY: 57122 AN XY: 74418

Gnomad4 AFR AF: 0.761

Gnomad4 AMR AF: 0.803

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.862

Gnomad4 SAS AF: 0.839

Gnomad4 FIN AF: 0.859

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.751

Alfa AF: 0.755 Hom.: 6552

Bravo AF: 0.752

Asia WGS AF: 0.826 AC: 2869 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.30
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1479924; hg19: chr4-123387600;