rs2139999

Positions:

• chr18-34438111-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;