rs1394349

chr18-51686238-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 0.0545 in 151,916 control chromosomes in the GnomAD database, including 271 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 0.054 (271 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.915

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0692 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: 0.0545 AC: 8274 AN: 151796 Hom.: 271 Cov.: 32

Gnomad AFR AF: 0.0373

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0436

Gnomad ASJ AF: 0.0795

Gnomad EAS AF: 0.0679

Gnomad SAS AF: 0.0588

Gnomad FIN AF: 0.0200

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0709

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0545 AC: 8272 AN: 151916 Hom.: 271 Cov.: 32 AF XY: 0.0524 AC XY: 3886 AN XY: 74220

Gnomad4 AFR AF: 0.0372

Gnomad4 AMR AF: 0.0435

Gnomad4 ASJ AF: 0.0795

Gnomad4 EAS AF: 0.0679

Gnomad4 SAS AF: 0.0587

Gnomad4 FIN AF: 0.0200

Gnomad4 NFE AF: 0.0709

Gnomad4 OTH AF: 0.0492

Alfa AF: 0.0693 Hom.: 282

Bravo AF: 0.0563

Asia WGS AF: 0.0550 AC: 189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.9
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1394349; hg19: chr18-49212608;