19-50905586-G-T

Variant names:

• chr19-50905586-G-T
• rs1701927

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 0.85 in 152,166 control chromosomes in the GnomAD database, including 56,191 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 (56191 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.931 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: 0.850 AC: 129178 AN: 152048 Hom.: 56148 Cov.: 31

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.850 AC: 129276 AN: 152166 Hom.: 56191 Cov.: 31 AF XY: 0.844 AC XY: 62809 AN XY: 74406

African (AFR) AF: 0.939 AC: 38981 AN: 41532

American (AMR) AF: 0.832 AC: 12718 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 3124 AN: 3470

East Asian (EAS) AF: 0.225 AC: 1162 AN: 5170

South Asian (SAS) AF: 0.733 AC: 3527 AN: 4810

European-Finnish (FIN) AF: 0.831 AC: 8798 AN: 10588

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.854 AC: 58063 AN: 67996

Other (OTH) AF: 0.862 AC: 1822 AN: 2114

Alfa AF: 0.850 Hom.: 207106

Bravo AF: 0.852

Asia WGS AF: 0.506 AC: 1766 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	0.37
DANN	Benign	0.42
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1701927; hg19: chr19-51408842;