18-66701917-C-T

Variant names:

• chr18-66701917-C-T
• rs1074258

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 0.608 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.448 AC: 18540 AN: 41398

American (AMR) AF: 0.632 AC: 9641 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2134 AN: 3468

East Asian (EAS) AF: 0.707 AC: 3639 AN: 5146

South Asian (SAS) AF: 0.597 AC: 2863 AN: 4798

European-Finnish (FIN) AF: 0.683 AC: 7204 AN: 10550

Middle Eastern (MID) AF: 0.638 AC: 185 AN: 290

European-Non Finnish (NFE) AF: 0.680 AC: 46170 AN: 67946

Other (OTH) AF: 0.608 AC: 1285 AN: 2112

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
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs1074258; hg19: chr18-64369154;