18-50219481-T-C

Position:

• chr18-50219481-T-C

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 0.21 in 152,042 control chromosomes in the GnomAD database, including 3,795 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 0.21 (3795 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31912 AN: 151924 Hom.: 3794 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.0431

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.210 AC: 31911 AN: 152042 Hom.: 3795 Cov.: 32 AF XY: 0.211 AC XY: 15664 AN XY: 74338

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.0431

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.231

Alfa AF: 0.243 Hom.: 2398

Bravo AF: 0.195

Asia WGS AF: 0.138 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.033
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1373185; hg19: chr18-47745851;