chr19-50901828-T-C

Variant names:

• chr19-50901828-T-C
• rs806023

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 0.354 in 151,924 control chromosomes in the GnomAD database, including 11,739 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 0.35 (11739 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186
• 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 = 0.473 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: 0.355 AC: 53835 AN: 151810 Hom.: 11745 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.0323

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.354 AC: 53833 AN: 151924 Hom.: 11739 Cov.: 31 AF XY: 0.354 AC XY: 26282 AN XY: 74214

African (AFR) AF: 0.121 AC: 5030 AN: 41492

American (AMR) AF: 0.426 AC: 6496 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1783 AN: 3472

East Asian (EAS) AF: 0.0328 AC: 170 AN: 5188

South Asian (SAS) AF: 0.265 AC: 1273 AN: 4802

European-Finnish (FIN) AF: 0.505 AC: 5307 AN: 10502

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32402 AN: 67902

Other (OTH) AF: 0.372 AC: 785 AN: 2108

Alfa AF: 0.302 Hom.: 950

Bravo AF: 0.341

Asia WGS AF: 0.147 AC: 514 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.19

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs806023; hg19: chr19-51405084;