18-1818384-A-G

Variant names:

• chr18-1818384-A-G
• rs2345595
• ENST00000653094.1:n.326-6394A>G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000653094.1(ENSG00000266602):​n.326-6394A>G variant causes a intron change. 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 0.00095 (2 hom., cov: 13)
• Consequence: ENSG00000266602 ENST00000653094.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 1 publications found

Genes affected

ENSG00000266602 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS2: High Homozygotes in GnomAd4 at 2 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653094.1. 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
	ENSG00000266602	ENST00000653094.1		n.326-6394A>G		intron	N/A
	ENSG00000266602	ENST00000653330.1		n.252-6394A>G		intron	N/A
	ENSG00000266602	ENST00000655815.1		n.252-6394A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000950 AC: 75 AN: 78968 Hom.: 2 Cov.: 13

Gnomad AFR AF: 0.000100

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000916

Gnomad ASJ AF: 0.000448

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0125

Gnomad NFE AF: 0.00151

Gnomad OTH AF: 0.00206

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

GnomAD4 genome AF: 0.000950 AC: 75 AN: 78988 Hom.: 2 Cov.: 13 AF XY: 0.000801 AC XY: 29 AN XY: 36226

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000100 AC: 2 AN: 19986

American (AMR) AF: 0.000917 AC: 6 AN: 6544

Ashkenazi Jewish (ASJ) AF: 0.000448 AC: 1 AN: 2230

East Asian (EAS) AF: 0.00 AC: 0 AN: 2566

South Asian (SAS) AF: 0.00 AC: 0 AN: 1704

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3246

Middle Eastern (MID) AF: 0.0139 AC: 2 AN: 144

European-Non Finnish (NFE) AF: 0.00151 AC: 62 AN: 41008

Other (OTH) AF: 0.00203 AC: 2 AN: 984

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.0000000000117691), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.000212 Hom.: 45

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.1
DANN	Benign	0.28

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: rs2345595;

hg19: chr18-1818385;