18-60061837-C-T

Position:

• chr18-60061837-C-T

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 0.488 in 151,896 control chromosomes in the GnomAD database, including 19,836 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 0.49 (19836 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.60061837C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74131 AN: 151778 Hom.: 19834 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.488 AC: 74162 AN: 151896 Hom.: 19836 Cov.: 31 AF XY: 0.492 AC XY: 36511 AN XY: 74202

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.512

Alfa AF: 0.540 Hom.: 12176

Bravo AF: 0.488

Asia WGS AF: 0.630 AC: 2190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.37
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3897644; hg19: chr18-57729069;