rs1394349

Variant names:

• chr18-51686238-G-A
• rs1394349

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 0.0545 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0372 AC: 1543 AN: 41458

American (AMR) AF: 0.0435 AC: 663 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.0795 AC: 276 AN: 3472

East Asian (EAS) AF: 0.0679 AC: 349 AN: 5142

South Asian (SAS) AF: 0.0587 AC: 282 AN: 4808

European-Finnish (FIN) AF: 0.0200 AC: 211 AN: 10532

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0709 AC: 4815 AN: 67948

Other (OTH) AF: 0.0492 AC: 104 AN: 2112

Alfa AF: 0.0686 Hom.: 355

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
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs1394349; hg19: chr18-49212608;