18-25748780-C-T

Variant names:

• chr18-25748780-C-T
• rs17799256

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 0.544 in 152,028 control chromosomes in the GnomAD database, including 23,015 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 0.54 (23015 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.605 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: 0.544 AC: 82600 AN: 151910 Hom.: 22990 Cov.: 33

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.544 AC: 82671 AN: 152028 Hom.: 23015 Cov.: 33 AF XY: 0.549 AC XY: 40811 AN XY: 74284

African (AFR) AF: 0.444 AC: 18402 AN: 41440

American (AMR) AF: 0.616 AC: 9408 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1926 AN: 3470

East Asian (EAS) AF: 0.607 AC: 3145 AN: 5178

South Asian (SAS) AF: 0.612 AC: 2950 AN: 4820

European-Finnish (FIN) AF: 0.603 AC: 6358 AN: 10544

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38521 AN: 67984

Other (OTH) AF: 0.544 AC: 1148 AN: 2110

Alfa AF: 0.560 Hom.: 81410

Bravo AF: 0.545

Asia WGS AF: 0.563 AC: 1958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.54
DANN	Benign	0.44
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs17799256; hg19: chr18-23328744;