rs10042348

Variant names:

• chr5-51922017-C-G
• rs10042348

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 0.667 in 151,926 control chromosomes in the GnomAD database, including 37,027 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 0.67 (37027 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803

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 = 0.806 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: 0.668 AC: 101365 AN: 151810 Hom.: 37025 Cov.: 30

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.803

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.667 AC: 101382 AN: 151926 Hom.: 37027 Cov.: 30 AF XY: 0.671 AC XY: 49840 AN XY: 74278

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.743

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.773

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.812

Gnomad4 OTH AF: 0.710

Alfa AF: 0.731 Hom.: 5341

Bravo AF: 0.646

Asia WGS AF: 0.621 AC: 2160 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	0.18
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10042348; hg19: chr5-51217851;