19-50902726-C-G

Variant names:

• chr19-50902726-C-G
• rs806019

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 0.846 in 152,070 control chromosomes in the GnomAD database, including 55,687 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 0.85 (55687 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128610 AN: 151952 Hom.: 55643 Cov.: 30

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.846 AC: 128714 AN: 152070 Hom.: 55687 Cov.: 30 AF XY: 0.842 AC XY: 62545 AN XY: 74322

African (AFR) AF: 0.929 AC: 38528 AN: 41480

American (AMR) AF: 0.830 AC: 12681 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3123 AN: 3468

East Asian (EAS) AF: 0.225 AC: 1162 AN: 5162

South Asian (SAS) AF: 0.749 AC: 3604 AN: 4814

European-Finnish (FIN) AF: 0.829 AC: 8749 AN: 10552

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.852 AC: 57967 AN: 67998

Other (OTH) AF: 0.861 AC: 1817 AN: 2110

Alfa AF: 0.807 Hom.: 2579

Bravo AF: 0.848

Asia WGS AF: 0.535 AC: 1864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.42
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs806019; hg19: chr19-51405982;