chr18-29026683-G-A

Variant names:

• chr18-29026683-G-A
• rs2155929

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 0.18 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
• Publications: 2 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.118 AC: 4893 AN: 41378

American (AMR) AF: 0.200 AC: 3042 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 721 AN: 3464

East Asian (EAS) AF: 0.432 AC: 2204 AN: 5104

South Asian (SAS) AF: 0.336 AC: 1615 AN: 4806

European-Finnish (FIN) AF: 0.155 AC: 1632 AN: 10516

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12745 AN: 67826

Other (OTH) AF: 0.182 AC: 382 AN: 2098

Alfa AF: 0.174 Hom.: 409

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
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs2155929; hg19: chr18-26606647;