18-50732122-G-A

Position:

• chr18-50732122-G-A

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 0.164 in 152,086 control chromosomes in the GnomAD database, including 2,219 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 0.16 (2219 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24930 AN: 151968 Hom.: 2223 Cov.: 33

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.164 AC: 24925 AN: 152086 Hom.: 2219 Cov.: 33 AF XY: 0.167 AC XY: 12380 AN XY: 74340

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.164

Alfa AF: 0.0883 Hom.: 136

Bravo AF: 0.155

Asia WGS AF: 0.223 AC: 772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4940007; hg19: chr18-48258492;