chr18-60236371-T-C

Position:

• chr18-60236371-T-C

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 0.202 in 151,878 control chromosomes in the GnomAD database, including 3,572 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 0.20 (3572 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.329 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: 0.202 AC: 30642 AN: 151762 Hom.: 3571 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.202 AC: 30643 AN: 151878 Hom.: 3572 Cov.: 31 AF XY: 0.199 AC XY: 14744 AN XY: 74242

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.212

Alfa AF: 0.250 Hom.: 6532

Bravo AF: 0.196

Asia WGS AF: 0.205 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12964203; hg19: chr18-57903604;