rs8109886

chr19-39252122-C-A

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 0.517 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.0815

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.507

Alfa AF: 0.461 Hom.: 23647

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8109886; hg19: chr19-39742762;