19-53276773-T-C

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 0.859 in 152,020 control chromosomes in the GnomAD database, including 56,289 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 0.86 (56289 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130487 AN: 151902 Hom.: 56259 Cov.: 30

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.859 AC: 130564 AN: 152020 Hom.: 56289 Cov.: 30 AF XY: 0.855 AC XY: 63493 AN XY: 74280

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.818

Gnomad4 FIN AF: 0.844

Gnomad4 NFE AF: 0.901

Gnomad4 OTH AF: 0.880

Alfa AF: 0.892 Hom.: 76945

Bravo AF: 0.858

Asia WGS AF: 0.777 AC: 2703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.3
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2965260; hg19: chr19-53780026;