rs1479924

Variant names:

• chr4-122466445-G-A
• rs1479924

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 24 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.761 AC: 31628 AN: 41544

American (AMR) AF: 0.803 AC: 12264 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2462 AN: 3468

East Asian (EAS) AF: 0.862 AC: 4464 AN: 5180

South Asian (SAS) AF: 0.839 AC: 4045 AN: 4820

European-Finnish (FIN) AF: 0.859 AC: 9103 AN: 10592

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 49029 AN: 67988

Other (OTH) AF: 0.751 AC: 1588 AN: 2114

Alfa AF: 0.755 Hom.: 6770

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
PhyloP100		-0.087

Splicing

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

Other links and lift over

dbSNP: rs1479924; hg19: chr4-123387600;