rs13439479

Variant names:

• chr8-42669270-A-T
• rs13439479

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 0.044 in 149,148 control chromosomes in the GnomAD database, including 182 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 0.044 (182 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0815 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: 0.0440 AC: 6556 AN: 149046 Hom.: 181 Cov.: 32

Gnomad AFR AF: 0.0499

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.0328

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0884

Gnomad FIN AF: 0.0500

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0386

Gnomad OTH AF: 0.0444

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

GnomAD4 genome AF: 0.0440 AC: 6564 AN: 149148 Hom.: 182 Cov.: 32 AF XY: 0.0446 AC XY: 3254 AN XY: 72958

Gnomad4 AFR AF: 0.0502

Gnomad4 AMR AF: 0.0328

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0885

Gnomad4 FIN AF: 0.0500

Gnomad4 NFE AF: 0.0386

Gnomad4 OTH AF: 0.0434

Alfa AF: 0.00825 Hom.: 1

Bravo AF: 0.0414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.8
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13439479; hg19: chr8-42524413;