rs10420357

Variant names:

• chr19-51461312-A-T
• rs10420357

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 0.144 in 152,062 control chromosomes in the GnomAD database, including 2,017 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 0.14 (2017 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 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: 0.143 AC: 21778 AN: 151944 Hom.: 2007 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0812

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0802

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.144 AC: 21822 AN: 152062 Hom.: 2017 Cov.: 32 AF XY: 0.144 AC XY: 10728 AN XY: 74330

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.0813

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.0802

Gnomad4 OTH AF: 0.150

Alfa AF: 0.114 Hom.: 152

Bravo AF: 0.150

Asia WGS AF: 0.167 AC: 580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10420357; hg19: chr19-51964566;