rs55799315

chr19-50860967-C-Gchr19-50860967-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 0.119 in 152,078 control chromosomes in the GnomAD database, including 1,328 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 0.12 (1328 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 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: 0.119 AC: 18139 AN: 151960 Hom.: 1329 Cov.: 32

Gnomad AFR AF: 0.0479

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.0958

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.0411

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.119 AC: 18149 AN: 152078 Hom.: 1328 Cov.: 32 AF XY: 0.122 AC XY: 9076 AN XY: 74322

Gnomad4 AFR AF: 0.0480

Gnomad4 AMR AF: 0.0957

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.0414

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.117

Alfa AF: 0.135 Hom.: 202

Bravo AF: 0.105

Asia WGS AF: 0.0730 AC: 254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	12
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55799315; hg19: chr19-51364223;