rs323118

Variant names:

• chr18-51678256-C-T
• rs323118

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.526

Alfa AF: 0.454 Hom.: 11399

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs323118; hg19: chr18-49204626;