18-60248736-T-C

Variant names:

• chr18-60248736-T-C
• rs752720

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;