rs442392

Positions:

• chr5-13603774-A-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 0.709 in 151,992 control chromosomes in the GnomAD database, including 39,500 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 0.71 (39500 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.782 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: 0.709 AC: 107688 AN: 151874 Hom.: 39481 Cov.: 32

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.709 AC: 107757 AN: 151992 Hom.: 39500 Cov.: 32 AF XY: 0.707 AC XY: 52517 AN XY: 74284

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.747

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.716

Alfa AF: 0.778 Hom.: 91535

Bravo AF: 0.702

Asia WGS AF: 0.570 AC: 1984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	16
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs442392; hg19: chr5-13603883;