rs10419982

Variant names:

• chr19-51293865-A-G
• rs10419982

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 0.562 in 152,054 control chromosomes in the GnomAD database, including 24,281 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 0.56 (24281 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.490

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.617 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: 0.562 AC: 85358 AN: 151936 Hom.: 24271 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.562 AC: 85399 AN: 152054 Hom.: 24281 Cov.: 32 AF XY: 0.559 AC XY: 41575 AN XY: 74336

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.560

Alfa AF: 0.575 Hom.: 35230

Bravo AF: 0.555

Asia WGS AF: 0.531 AC: 1848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.0
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10419982; hg19: chr19-51797119;