18-60559879-T-C

Variant names:

• chr18-60559879-T-C
• rs1430387

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.329 AC: 13621 AN: 41464

American (AMR) AF: 0.518 AC: 7905 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1501 AN: 3472

East Asian (EAS) AF: 0.728 AC: 3768 AN: 5176

South Asian (SAS) AF: 0.633 AC: 3046 AN: 4814

European-Finnish (FIN) AF: 0.504 AC: 5324 AN: 10566

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29334 AN: 67920

Other (OTH) AF: 0.432 AC: 912 AN: 2112

Alfa AF: 0.429 Hom.: 29426

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
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs1430387; hg19: chr18-58227112;