18-50219481-T-C

Variant names:

• chr18-50219481-T-C
• rs1373185

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 0.21 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.114 AC: 4743 AN: 41480

American (AMR) AF: 0.173 AC: 2636 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 921 AN: 3470

East Asian (EAS) AF: 0.0431 AC: 223 AN: 5180

South Asian (SAS) AF: 0.242 AC: 1167 AN: 4820

European-Finnish (FIN) AF: 0.312 AC: 3293 AN: 10556

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18072 AN: 67948

Other (OTH) AF: 0.231 AC: 486 AN: 2102

Alfa AF: 0.246 Hom.: 3741

Bravo AF: 0.195

Asia WGS AF: 0.138 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.033
DANN	Benign	0.31
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1373185; hg19: chr18-47745851;