18-46284605-C-T

Variant names:

• chr18-46284605-C-T
• rs726131

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 0.336 in 152,076 control chromosomes in the GnomAD database, including 10,326 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 0.34 (10326 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.461 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: 0.337 AC: 51192 AN: 151958 Hom.: 10339 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.0492

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.336 AC: 51170 AN: 152076 Hom.: 10326 Cov.: 32 AF XY: 0.336 AC XY: 25009 AN XY: 74354

African (AFR) AF: 0.137 AC: 5686 AN: 41490

American (AMR) AF: 0.295 AC: 4496 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1709 AN: 3470

East Asian (EAS) AF: 0.0491 AC: 255 AN: 5192

South Asian (SAS) AF: 0.477 AC: 2299 AN: 4816

European-Finnish (FIN) AF: 0.434 AC: 4586 AN: 10578

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30720 AN: 67952

Other (OTH) AF: 0.383 AC: 808 AN: 2108

Alfa AF: 0.407 Hom.: 40625

Bravo AF: 0.310

Asia WGS AF: 0.244 AC: 851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.20
DANN	Benign	0.83
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs726131; hg19: chr18-43864568;