rs2139999

Variant names:

• chr18-34438111-A-G
• rs2139999

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 0.13 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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

African (AFR) AF: 0.0320 AC: 1329 AN: 41570

American (AMR) AF: 0.107 AC: 1635 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3470

East Asian (EAS) AF: 0.0843 AC: 437 AN: 5186

South Asian (SAS) AF: 0.126 AC: 610 AN: 4828

European-Finnish (FIN) AF: 0.226 AC: 2388 AN: 10580

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12467 AN: 67996

Other (OTH) AF: 0.134 AC: 283 AN: 2114

Alfa AF: 0.133 Hom.: 748

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
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs2139999; hg19: chr18-32018075;