19-53276773-T-C

Variant names:

• chr19-53276773-T-C
• rs2965260

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;