rs323118

Variant names:

• chr18-51678256-C-T
• rs323118

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 0.575 in 152,096 control chromosomes in the GnomAD database, including 27,750 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 0.57 (27750 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.444
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 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: 0.575 AC: 87349 AN: 151978 Hom.: 27703 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.575 AC: 87447 AN: 152096 Hom.: 27750 Cov.: 32 AF XY: 0.577 AC XY: 42896 AN XY: 74346

African (AFR) AF: 0.823 AC: 34164 AN: 41534

American (AMR) AF: 0.536 AC: 8178 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1567 AN: 3472

East Asian (EAS) AF: 0.950 AC: 4918 AN: 5178

South Asian (SAS) AF: 0.545 AC: 2626 AN: 4816

European-Finnish (FIN) AF: 0.449 AC: 4744 AN: 10558

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29552 AN: 67952

Other (OTH) AF: 0.526 AC: 1113 AN: 2114

Alfa AF: 0.477 Hom.: 18326

Bravo AF: 0.597

Asia WGS AF: 0.753 AC: 2616 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	1.6
DANN	Benign	0.43
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs323118; hg19: chr18-49204626;