chr19-266544-C-T

Position:

• chr19-266544-C-T

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 0.65 in 152,110 control chromosomes in the GnomAD database, including 33,987 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 0.65 (33987 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98711 AN: 151992 Hom.: 33943 Cov.: 33

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.650 AC: 98803 AN: 152110 Hom.: 33987 Cov.: 33 AF XY: 0.643 AC XY: 47804 AN XY: 74370

Gnomad4 AFR AF: 0.851

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.640

Alfa AF: 0.635 Hom.: 5190

Bravo AF: 0.651

Asia WGS AF: 0.371 AC: 1293 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8106462; hg19: chr19-266544;