chr18-66137654-T-C

Variant names:

• chr18-66137654-T-C
• rs1388176

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 0.852 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.601 AC: 24857 AN: 41378

American (AMR) AF: 0.893 AC: 13619 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.975 AC: 3385 AN: 3472

East Asian (EAS) AF: 0.695 AC: 3580 AN: 5150

South Asian (SAS) AF: 0.867 AC: 4169 AN: 4808

European-Finnish (FIN) AF: 0.938 AC: 9942 AN: 10596

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.983 AC: 66879 AN: 68018

Other (OTH) AF: 0.865 AC: 1826 AN: 2112

Alfa AF: 0.947 Hom.: 79827

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
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs1388176; hg19: chr18-63804890;