19-50852909-C-T

Variant names:

• chr19-50852909-C-T
• rs266861

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 0.743 in 151,082 control chromosomes in the GnomAD database, including 42,078 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 0.74 (42078 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.762 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: 0.743 AC: 112153 AN: 150964 Hom.: 42055 Cov.: 27

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.657

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.743 AC: 112232 AN: 151082 Hom.: 42078 Cov.: 27 AF XY: 0.741 AC XY: 54584 AN XY: 73662

African (AFR) AF: 0.744 AC: 30534 AN: 41054

American (AMR) AF: 0.705 AC: 10696 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2314 AN: 3470

East Asian (EAS) AF: 0.515 AC: 2636 AN: 5118

South Asian (SAS) AF: 0.563 AC: 2702 AN: 4798

European-Finnish (FIN) AF: 0.872 AC: 8936 AN: 10242

Middle Eastern (MID) AF: 0.637 AC: 186 AN: 292

European-Non Finnish (NFE) AF: 0.767 AC: 52129 AN: 67924

Other (OTH) AF: 0.708 AC: 1486 AN: 2100

Alfa AF: 0.756 Hom.: 32585

Bravo AF: 0.730

Asia WGS AF: 0.558 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.1
DANN	Benign	0.17
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs266861; hg19: chr19-51356165;