rs8109886

Variant names:

• chr19-39252122-C-A
• rs8109886

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 0.517 in 151,964 control chromosomes in the GnomAD database, including 22,931 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 0.52 (22931 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.791
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.775 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: 0.517 AC: 78533 AN: 151844 Hom.: 22891 Cov.: 32

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.0811

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.517 AC: 78627 AN: 151964 Hom.: 22931 Cov.: 32 AF XY: 0.506 AC XY: 37580 AN XY: 74258

African (AFR) AF: 0.783 AC: 32410 AN: 41418

American (AMR) AF: 0.490 AC: 7480 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1946 AN: 3464

East Asian (EAS) AF: 0.0815 AC: 422 AN: 5180

South Asian (SAS) AF: 0.326 AC: 1565 AN: 4806

European-Finnish (FIN) AF: 0.334 AC: 3526 AN: 10548

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29593 AN: 67956

Other (OTH) AF: 0.507 AC: 1069 AN: 2110

Alfa AF: 0.475 Hom.: 38249

Bravo AF: 0.544

Asia WGS AF: 0.245 AC: 858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.23
DANN	Benign	0.63
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs8109886; hg19: chr19-39742762;