Genetic Variant ENST00000445418.1:n.289-865C>T (chr2-679179-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.19

Publications

10 publications found

Variant links:

Genes affected

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

TMEM18-DT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM18-DT	NR_183416.1 link	n.116-865C>T		intron_variant	Intron 1 of 2
TMEM18-DT	NR_183417.1 link	n.103-865C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TMEM18-DT	ENST00000445418.1 link	n.289-865C>T	intron_variant	Intron 1 of 2	2
TMEM18-DT	ENST00000783571.1 link	n.172-865C>T	intron_variant	Intron 1 of 2
TMEM18-DT	ENST00000783572.1 link	n.119-865C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0934

AC:

14204

AN:

152074

Hom.:

645

Cov.:

show subpopulations

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.:

AF XY:

0.0914

AC XY:

6801

AN XY:

74396

show subpopulations

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:

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.105

AC:

7161

AN:

68014

Other (OTH)

AF:

0.0921

AC:

194

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

648

1296

1945

2593

3241

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

168

336

504

672

840

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.0

(source)

DANN

Benign

0.79

PhyloP100

-1.2

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over