chr19-53276773-T-C

Variant names:

• chr19-53276773-T-C
• rs2965260

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 0.859 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.799 AC: 33129 AN: 41450

American (AMR) AF: 0.867 AC: 13257 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3164 AN: 3468

East Asian (EAS) AF: 0.784 AC: 4035 AN: 5148

South Asian (SAS) AF: 0.818 AC: 3927 AN: 4800

European-Finnish (FIN) AF: 0.844 AC: 8922 AN: 10568

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.901 AC: 61239 AN: 67984

Other (OTH) AF: 0.880 AC: 1862 AN: 2116

Alfa AF: 0.883 Hom.: 120362

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
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs2965260; hg19: chr19-53780026;