19-6941856-G-A

Variant names:

• chr19-6941856-G-A
• rs465543

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 0.697 in 151,868 control chromosomes in the GnomAD database, including 37,097 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 0.70 (37097 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105764 AN: 151750 Hom.: 37078 Cov.: 30

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.697 AC: 105823 AN: 151868 Hom.: 37097 Cov.: 30 AF XY: 0.697 AC XY: 51701 AN XY: 74202

African (AFR) AF: 0.618 AC: 25546 AN: 41338

American (AMR) AF: 0.704 AC: 10755 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 2467 AN: 3470

East Asian (EAS) AF: 0.687 AC: 3543 AN: 5158

South Asian (SAS) AF: 0.666 AC: 3207 AN: 4812

European-Finnish (FIN) AF: 0.726 AC: 7667 AN: 10554

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50188 AN: 67954

Other (OTH) AF: 0.678 AC: 1429 AN: 2108

Alfa AF: 0.718 Hom.: 26572

Bravo AF: 0.693

Asia WGS AF: 0.617 AC: 2146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.35
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs465543; hg19: chr19-6941867;