rs10421086

Variant names:

• chr19-51731607-T-C
• rs10421086

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.506 AC: 20962 AN: 41446

American (AMR) AF: 0.455 AC: 6955 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1265 AN: 3470

East Asian (EAS) AF: 0.739 AC: 3821 AN: 5174

South Asian (SAS) AF: 0.418 AC: 2012 AN: 4818

European-Finnish (FIN) AF: 0.359 AC: 3795 AN: 10572

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23408 AN: 67966

Other (OTH) AF: 0.402 AC: 849 AN: 2110

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
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs10421086; hg19: chr19-52234860;