18-66137654-T-C

Variant names:

• chr18-66137654-T-C
• rs1388176

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.490

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;