rs1479923

Positions:

• chr4-122449232-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;