rs3019982

Variant names:

• chr8-107024728-A-C
• rs3019982

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 0.731 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.637 AC: 26315 AN: 41342

American (AMR) AF: 0.731 AC: 11161 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2694 AN: 3468

East Asian (EAS) AF: 0.523 AC: 2676 AN: 5120

South Asian (SAS) AF: 0.667 AC: 3207 AN: 4810

European-Finnish (FIN) AF: 0.805 AC: 8486 AN: 10546

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54037 AN: 67954

Other (OTH) AF: 0.734 AC: 1542 AN: 2102

Alfa AF: 0.753 Hom.: 5599

Bravo AF: 0.722

Asia WGS AF: 0.648 AC: 2253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.35
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs3019982; hg19: chr8-108036956;