2-679179-C-T

Variant names:

• chr2-679179-C-T
• rs1320333
• ENST00000445418.1:n.289-865C>T

Variant summary

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

The ENST00000445418.1(TMEM18-DT):​n.289-865C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0934 in 152,192 control chromosomes in the GnomAD database, including 648 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 0.093 (648 hom., cov: 32)
• Consequence: TMEM18-DT ENST00000445418.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 10 publications found

Genes affected

TMEM18-DT (HGNC:54481): (TMEM18 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445418.1. 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
	TMEM18-DT	NR_183416.1		n.116-865C>T		intron	N/A
	TMEM18-DT	NR_183417.1		n.103-865C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM18-DT	ENST00000445418.1	TSL:2	n.289-865C>T		intron	N/A
	TMEM18-DT	ENST00000783571.1		n.172-865C>T		intron	N/A
	TMEM18-DT	ENST00000783572.1		n.119-865C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0934 AC: 14204 AN: 152074 Hom.: 645 Cov.: 32

Gnomad AFR AF: 0.0925

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0787

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.0833

Gnomad FIN AF: 0.0856

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0931

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

GnomAD4 genome AF: 0.0934 AC: 14214 AN: 152192 Hom.: 648 Cov.: 32 AF XY: 0.0914 AC XY: 6801 AN XY: 74396

African (AFR) AF: 0.0926 AC: 3844 AN: 41508

American (AMR) AF: 0.0785 AC: 1201 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 359 AN: 3470

East Asian (EAS) AF: 0.0150 AC: 78 AN: 5186

South Asian (SAS) AF: 0.0832 AC: 401 AN: 4822

European-Finnish (FIN) AF: 0.0856 AC: 906 AN: 10590

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7161 AN: 68014

Other (OTH) AF: 0.0921 AC: 194 AN: 2106

Alfa AF: 0.100 Hom.: 2509

Bravo AF: 0.0925

Asia WGS AF: 0.0670 AC: 232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.79
PhyloP100		-1.2

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: rs1320333;

hg19: chr2-679179;