18-66701917-C-T

Position:

• chr18-66701917-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 0.608 in 151,872 control chromosomes in the GnomAD database, including 28,813 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 0.61 (28813 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92310 AN: 151752 Hom.: 28790 Cov.: 31

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.608 AC: 92381 AN: 151872 Hom.: 28813 Cov.: 31 AF XY: 0.610 AC XY: 45233 AN XY: 74200

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.608

Alfa AF: 0.647 Hom.: 5460

Bravo AF: 0.600

Asia WGS AF: 0.615 AC: 2135 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.021
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1074258; hg19: chr18-64369154;