19-50852909-C-T

Variant names:

• chr19-50852909-C-T
• rs266861

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.872

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.708

Alfa AF: 0.751 Hom.: 16372

Bravo AF: 0.730

Asia WGS AF: 0.558 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs266861; hg19: chr19-51356165;