rs4942925

chr13-32807106-T-C

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 0.363 in 152,106 control chromosomes in the GnomAD database, including 10,742 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 0.36 (10742 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55223 AN: 151988 Hom.: 10745 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.363 AC: 55234 AN: 152106 Hom.: 10742 Cov.: 32 AF XY: 0.360 AC XY: 26777 AN XY: 74350

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.375

Alfa AF: 0.414 Hom.: 17555

Bravo AF: 0.357

Asia WGS AF: 0.176 AC: 618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.9
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: rs4942925; hg19: chr13-33381244;