rs8106462

Variant names:

• chr19-266544-C-T
• rs8106462

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 0.65 in 152,110 control chromosomes in the GnomAD database, including 33,987 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 0.65 (33987 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 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: 0.649 AC: 98711 AN: 151992 Hom.: 33943 Cov.: 33

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.650 AC: 98803 AN: 152110 Hom.: 33987 Cov.: 33 AF XY: 0.643 AC XY: 47804 AN XY: 74370

African (AFR) AF: 0.851 AC: 35364 AN: 41532

American (AMR) AF: 0.539 AC: 8232 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2414 AN: 3472

East Asian (EAS) AF: 0.140 AC: 724 AN: 5166

South Asian (SAS) AF: 0.473 AC: 2280 AN: 4824

European-Finnish (FIN) AF: 0.652 AC: 6879 AN: 10550

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40714 AN: 67970

Other (OTH) AF: 0.640 AC: 1351 AN: 2110

Alfa AF: 0.613 Hom.: 10019

Bravo AF: 0.651

Asia WGS AF: 0.371 AC: 1293 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.94
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs8106462; hg19: chr19-266544;