18-29102295-T-G

Variant names:

• chr18-29102295-T-G
• rs1833422
• ENST00000789716.1:n.273-16853A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000789716.1(ENSG00000302813):​n.273-16853A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000302813 ENST00000789716.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.29
• Publications: 3 publications found

Genes affected

ENSG00000302813 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789716.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302813	ENST00000789716.1		n.273-16853A>C		intron	N/A

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

African (AFR) AF: 0.411 AC: 16975 AN: 41252

American (AMR) AF: 0.777 AC: 11688 AN: 15044

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2960 AN: 3442

East Asian (EAS) AF: 0.973 AC: 4945 AN: 5082

South Asian (SAS) AF: 0.810 AC: 3895 AN: 4808

European-Finnish (FIN) AF: 0.740 AC: 7814 AN: 10564

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.808 AC: 54400 AN: 67324

Other (OTH) AF: 0.763 AC: 1597 AN: 2094

Alfa AF: 0.784 Hom.: 78342

Bravo AF: 0.693

Asia WGS AF: 0.857 AC: 2980 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.69
PhyloP100		2.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1833422;

hg19: chr18-26682259;