rs1560719

Variant names:

• chr19-50897580-A-G
• rs1560719

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 0.516 in 151,814 control chromosomes in the GnomAD database, including 24,060 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 0.52 (24060 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 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: 0.516 AC: 78267 AN: 151698 Hom.: 24007 Cov.: 31

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.516 AC: 78378 AN: 151814 Hom.: 24060 Cov.: 31 AF XY: 0.509 AC XY: 37724 AN XY: 74178

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.509

Alfa AF: 0.500 Hom.: 3366

Bravo AF: 0.537

Asia WGS AF: 0.397 AC: 1383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1560719; hg19: chr19-51400836; COSMIC: COSV74139927;