rs62094879

Variant names:

• chr18-57829073-C-T
• rs62094879

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 0.143 in 151,850 control chromosomes in the GnomAD database, including 1,840 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 0.14 (1840 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.188 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: 0.143 AC: 21714 AN: 151730 Hom.: 1839 Cov.: 29

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.00233

Gnomad SAS AF: 0.0989

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.143 AC: 21717 AN: 151850 Hom.: 1840 Cov.: 29 AF XY: 0.136 AC XY: 10074 AN XY: 74182

Gnomad4 AFR AF: 0.0948

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.00233

Gnomad4 SAS AF: 0.0984

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.153

Alfa AF: 0.165 Hom.: 280

Bravo AF: 0.143

Asia WGS AF: 0.0620 AC: 217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs62094879; hg19: chr18-55496305;