18-75815681-C-T

Variant names:

• chr18-75815681-C-T
• rs1017745

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 0.563 in 151,946 control chromosomes in the GnomAD database, including 24,979 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 0.56 (24979 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.775 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: 0.563 AC: 85491 AN: 151826 Hom.: 24956 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.563 AC: 85549 AN: 151946 Hom.: 24979 Cov.: 32 AF XY: 0.572 AC XY: 42451 AN XY: 74276

African (AFR) AF: 0.425 AC: 17603 AN: 41414

American (AMR) AF: 0.651 AC: 9951 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1996 AN: 3468

East Asian (EAS) AF: 0.795 AC: 4095 AN: 5148

South Asian (SAS) AF: 0.705 AC: 3394 AN: 4816

European-Finnish (FIN) AF: 0.666 AC: 7027 AN: 10556

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.585 AC: 39734 AN: 67950

Other (OTH) AF: 0.583 AC: 1229 AN: 2108

Alfa AF: 0.576 Hom.: 45454

Bravo AF: 0.557

Asia WGS AF: 0.726 AC: 2518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.45
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs1017745; hg19: chr18-73527636;