rs3019982

Positions:

• chr8-107024728-A-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;