rs2155929

Positions:

• chr18-29026683-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 0.18 in 151,590 control chromosomes in the GnomAD database, including 2,844 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 0.18 (2844 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 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: 0.181 AC: 27341 AN: 151472 Hom.: 2849 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.180 AC: 27343 AN: 151590 Hom.: 2844 Cov.: 32 AF XY: 0.185 AC XY: 13703 AN XY: 74054

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.182

Alfa AF: 0.176 Hom.: 403

Bravo AF: 0.174

Asia WGS AF: 0.357 AC: 1238 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2155929; hg19: chr18-26606647;