chr19-50905502-G-T

Variant names:

• chr19-50905502-G-T
• rs1701926

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 152,198 control chromosomes in the GnomAD database, including 56,226 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 (56226 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304
• Publications: 2 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.850 AC: 129230 AN: 152080 Hom.: 56176 Cov.: 32

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.850 AC: 129340 AN: 152198 Hom.: 56226 Cov.: 32 AF XY: 0.844 AC XY: 62825 AN XY: 74396

African (AFR) AF: 0.939 AC: 39005 AN: 41556

American (AMR) AF: 0.832 AC: 12733 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 3126 AN: 3472

East Asian (EAS) AF: 0.225 AC: 1160 AN: 5166

South Asian (SAS) AF: 0.734 AC: 3530 AN: 4806

European-Finnish (FIN) AF: 0.831 AC: 8786 AN: 10570

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

European-Non Finnish (NFE) AF: 0.854 AC: 58084 AN: 68014

Other (OTH) AF: 0.868 AC: 1835 AN: 2114

Alfa AF: 0.861 Hom.: 7363

Bravo AF: 0.852

Asia WGS AF: 0.525 AC: 1830 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	0.58
DANN	Benign	0.12
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1701926; hg19: chr19-51408758;