ENST00000653094.1:n.326-6394A>C

Variant names:

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

Variant summary

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

The ENST00000653094.1(ENSG00000266602):​n.326-6394A>C 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 0.075 (252 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0905 is higher than 0.05.

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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000266602	ENST00000653094.1		n.326-6394A>C		intron	N/A
	ENSG00000266602	ENST00000653330.1		n.252-6394A>C		intron	N/A
	ENSG00000266602	ENST00000655815.1		n.252-6394A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0753 AC: 5886 AN: 78206 Hom.: 251 Cov.: 13

Gnomad AFR AF: 0.0924

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0967

Gnomad ASJ AF: 0.0577

Gnomad EAS AF: 0.000777

Gnomad SAS AF: 0.0331

Gnomad FIN AF: 0.0542

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0720

Gnomad OTH AF: 0.0800

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

GnomAD4 genome AF: 0.0752 AC: 5884 AN: 78226 Hom.: 252 Cov.: 13 AF XY: 0.0746 AC XY: 2677 AN XY: 35866

African (AFR) AF: 0.0923 AC: 1815 AN: 19662

American (AMR) AF: 0.0968 AC: 627 AN: 6476

Ashkenazi Jewish (ASJ) AF: 0.0577 AC: 128 AN: 2220

East Asian (EAS) AF: 0.000779 AC: 2 AN: 2566

South Asian (SAS) AF: 0.0329 AC: 56 AN: 1700

European-Finnish (FIN) AF: 0.0542 AC: 175 AN: 3226

Middle Eastern (MID) AF: 0.0845 AC: 12 AN: 142

European-Non Finnish (NFE) AF: 0.0720 AC: 2928 AN: 40686

Other (OTH) AF: 0.0789 AC: 77 AN: 976

Alfa AF: 0.0177 Hom.: 45

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.9
DANN	Benign	0.32

Splicing

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

Other links and lift over

dbSNP: rs2345595; hg19: chr18-1818385;