rs10421086

Positions:

• chr19-51731607-T-C
• chr19-51731607-T-G

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 0.416 in 152,038 control chromosomes in the GnomAD database, including 13,837 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 0.42 (13837 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 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: 0.416 AC: 63224 AN: 151920 Hom.: 13812 Cov.: 33

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.416 AC: 63294 AN: 152038 Hom.: 13837 Cov.: 33 AF XY: 0.419 AC XY: 31129 AN XY: 74322

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.402

Alfa AF: 0.387 Hom.: 1432

Bravo AF: 0.426

Asia WGS AF: 0.570 AC: 1983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.2
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10421086; hg19: chr19-52234860;