18-75730496-C-T

Variant names:

• chr18-75730496-C-T
• rs1943212

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 0.873 in 152,142 control chromosomes in the GnomAD database, including 59,395 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 0.87 (59395 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.957 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: 0.873 AC: 132752 AN: 152026 Hom.: 59380 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.958

Gnomad EAS AF: 0.958

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.895

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

GnomAD4 genome AF: 0.873 AC: 132807 AN: 152142 Hom.: 59395 Cov.: 32 AF XY: 0.875 AC XY: 65082 AN XY: 74388

African (AFR) AF: 0.654 AC: 27093 AN: 41424

American (AMR) AF: 0.938 AC: 14340 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.958 AC: 3327 AN: 3472

East Asian (EAS) AF: 0.958 AC: 4951 AN: 5170

South Asian (SAS) AF: 0.916 AC: 4421 AN: 4826

European-Finnish (FIN) AF: 0.952 AC: 10106 AN: 10610

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.963 AC: 65530 AN: 68038

Other (OTH) AF: 0.894 AC: 1890 AN: 2114

Alfa AF: 0.904 Hom.: 3192

Bravo AF: 0.861

Asia WGS AF: 0.919 AC: 3196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.1
DANN	Benign	0.65
PhyloP100		-0.067

Splicing

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

Other links and lift over

dbSNP: rs1943212; hg19: chr18-73442451;