rs1479923

Variant names:

• chr4-122449232-G-A
• rs1479923

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 0.248 in 152,062 control chromosomes in the GnomAD database, including 5,694 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 0.25 (5694 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.488 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: 0.248 AC: 37747 AN: 151944 Hom.: 5680 Cov.: 31

Gnomad AFR AF: 0.0737

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.248 AC: 37781 AN: 152062 Hom.: 5694 Cov.: 31 AF XY: 0.254 AC XY: 18904 AN XY: 74320

Gnomad4 AFR AF: 0.0738

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.302

Alfa AF: 0.298 Hom.: 12274

Bravo AF: 0.237

Asia WGS AF: 0.422 AC: 1468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1479923; hg19: chr4-123370387;