18-60559879-T-C

Position:

• chr18-60559879-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 0.433 in 151,986 control chromosomes in the GnomAD database, including 14,955 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 0.43 (14955 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.555

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65849 AN: 151868 Hom.: 14956 Cov.: 33

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.433 AC: 65860 AN: 151986 Hom.: 14955 Cov.: 33 AF XY: 0.444 AC XY: 32984 AN XY: 74310

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.432

Alfa AF: 0.435 Hom.: 19354

Bravo AF: 0.429

Asia WGS AF: 0.650 AC: 2246 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	13
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1430387; hg19: chr18-58227112;