rs2006747

chr18-50441988-G-Cchr18-50441988-G-T

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 0.442 in 152,054 control chromosomes in the GnomAD database, including 15,394 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 0.44 (15394 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 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: 0.442 AC: 67093 AN: 151934 Hom.: 15365 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.442 AC: 67180 AN: 152054 Hom.: 15394 Cov.: 32 AF XY: 0.440 AC XY: 32703 AN XY: 74312

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.445

Alfa AF: 0.257 Hom.: 571

Bravo AF: 0.448

Asia WGS AF: 0.505 AC: 1759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.6
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2006747; hg19: chr18-47968358;