chr18-62458879-T-C

Variant names:

• chr18-62458879-T-C
• rs694419

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 0.535 in 152,116 control chromosomes in the GnomAD database, including 22,570 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 0.53 (22570 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81249 AN: 151998 Hom.: 22540 Cov.: 33

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.535 AC: 81321 AN: 152116 Hom.: 22570 Cov.: 33 AF XY: 0.546 AC XY: 40595 AN XY: 74348

African (AFR) AF: 0.513 AC: 21300 AN: 41480

American (AMR) AF: 0.603 AC: 9214 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1908 AN: 3472

East Asian (EAS) AF: 0.937 AC: 4852 AN: 5176

South Asian (SAS) AF: 0.831 AC: 4013 AN: 4830

European-Finnish (FIN) AF: 0.542 AC: 5726 AN: 10574

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32631 AN: 67984

Other (OTH) AF: 0.551 AC: 1165 AN: 2116

Alfa AF: 0.515 Hom.: 33678

Bravo AF: 0.537

Asia WGS AF: 0.800 AC: 2778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.39
DANN	Benign	0.32
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs694419; hg19: chr18-60126112;