18-60248736-T-C

Position:

• chr18-60248736-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 0.518 in 151,990 control chromosomes in the GnomAD database, including 21,099 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 0.52 (21099 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.618 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: 0.518 AC: 78674 AN: 151872 Hom.: 21076 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.518 AC: 78734 AN: 151990 Hom.: 21099 Cov.: 32 AF XY: 0.512 AC XY: 38010 AN XY: 74284

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.488

Alfa AF: 0.502 Hom.: 25064

Bravo AF: 0.516

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs752720; hg19: chr18-57915969;