chr18-66137654-T-C

Position:

• chr18-66137654-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 0.852 in 151,990 control chromosomes in the GnomAD database, including 57,186 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 0.85 (57186 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.490

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.66137654T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129348 AN: 151874 Hom.: 57150 Cov.: 30

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.975

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.983

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.852 AC: 129435 AN: 151990 Hom.: 57186 Cov.: 30 AF XY: 0.850 AC XY: 63180 AN XY: 74290

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.975

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.867

Gnomad4 FIN AF: 0.938

Gnomad4 NFE AF: 0.983

Gnomad4 OTH AF: 0.865

Alfa AF: 0.951 Hom.: 67829

Bravo AF: 0.837

Asia WGS AF: 0.794 AC: 2751 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	17
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1388176; hg19: chr18-63804890;