chr18-62608007-C-T

Position:

• chr18-62608007-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 0.134 in 152,122 control chromosomes in the GnomAD database, including 1,519 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 0.13 (1519 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20418 AN: 152004 Hom.: 1522 Cov.: 32

Gnomad AFR AF: 0.0741

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.134 AC: 20429 AN: 152122 Hom.: 1519 Cov.: 32 AF XY: 0.136 AC XY: 10079 AN XY: 74372

Gnomad4 AFR AF: 0.0743

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.163

Alfa AF: 0.149 Hom.: 925

Bravo AF: 0.135

Asia WGS AF: 0.220 AC: 765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515988; hg19: chr18-60275240;