rs1373185

Variant names:

• chr18-50219481-T-C
• rs1373185

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;