18-29102295-T-G

Position:

• chr18-29102295-T-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 0.697 in 150,816 control chromosomes in the GnomAD database, including 39,035 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 0.70 (39035 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.29

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.29102295T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.698 AC: 105128 AN: 150698 Hom.: 39018 Cov.: 30

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.697 AC: 105184 AN: 150816 Hom.: 39035 Cov.: 30 AF XY: 0.700 AC XY: 51555 AN XY: 73624

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.777

Gnomad4 ASJ AF: 0.860

Gnomad4 EAS AF: 0.973

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.740

Gnomad4 NFE AF: 0.808

Gnomad4 OTH AF: 0.763

Alfa AF: 0.796 Hom.: 65335

Bravo AF: 0.693

Asia WGS AF: 0.857 AC: 2980 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1833422; hg19: chr18-26682259;