rs3019982

Variant names:

• chr8-107024728-A-C
• rs3019982

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 0.731 in 151,818 control chromosomes in the GnomAD database, including 41,081 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 0.73 (41081 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.79 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: 0.731 AC: 110955 AN: 151700 Hom.: 41055 Cov.: 29

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.731 AC: 111028 AN: 151818 Hom.: 41081 Cov.: 29 AF XY: 0.730 AC XY: 54173 AN XY: 74200

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.777

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.734

Alfa AF: 0.758 Hom.: 5447

Bravo AF: 0.722

Asia WGS AF: 0.648 AC: 2253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3019982; hg19: chr8-108036956;