rs2139999

Variant names:

• chr18-34438111-A-G
• rs2139999

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 0.13 in 152,232 control chromosomes in the GnomAD database, including 1,641 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 0.13 (1641 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.676

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.181 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: 0.130 AC: 19810 AN: 152114 Hom.: 1640 Cov.: 32

Gnomad AFR AF: 0.0320

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0843

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.130 AC: 19812 AN: 152232 Hom.: 1641 Cov.: 32 AF XY: 0.130 AC XY: 9690 AN XY: 74426

Gnomad4 AFR AF: 0.0320

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.0843

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.134

Alfa AF: 0.154 Hom.: 598

Bravo AF: 0.119

Asia WGS AF: 0.105 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.10
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2139999; hg19: chr18-32018075;