18-46318465-C-T

Variant names:

• chr18-46318465-C-T
• rs920783

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 0.431 in 151,848 control chromosomes in the GnomAD database, including 16,299 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 0.43 (16299 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 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: 0.432 AC: 65502 AN: 151730 Hom.: 16300 Cov.: 30

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.431 AC: 65517 AN: 151848 Hom.: 16299 Cov.: 30 AF XY: 0.436 AC XY: 32345 AN XY: 74204

African (AFR) AF: 0.162 AC: 6701 AN: 41444

American (AMR) AF: 0.514 AC: 7843 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2024 AN: 3468

East Asian (EAS) AF: 0.532 AC: 2734 AN: 5142

South Asian (SAS) AF: 0.406 AC: 1954 AN: 4810

European-Finnish (FIN) AF: 0.585 AC: 6165 AN: 10532

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36432 AN: 67886

Other (OTH) AF: 0.458 AC: 966 AN: 2108

Alfa AF: 0.501 Hom.: 56493

Bravo AF: 0.415

Asia WGS AF: 0.444 AC: 1544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.34
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs920783; hg19: chr18-43898428;