dbSNP rs8088001: THOC1-DT:n.632-4889T>G (chr18-287705-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000819908.1(THOC1-DT):n.632-4889T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,108 control chromosomes in the GnomAD database, including 2,121 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 0.14 ( 2121 hom., cov: 32)

Consequence

THOC1-DT
ENST00000819908.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.190

Publications

6 publications found

Variant links:

Genes affected

THOC1-DT (HGNC:55334): (THOC1 divergent transcript)

THOC1-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=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
THOC1-DT	ENST00000819908.1 link	n.632-4889T>G	intron_variant	Intron 2 of 2
THOC1-DT	ENST00000819909.1 link	n.762-4889T>G	intron_variant	Intron 1 of 1
THOC1-DT	ENST00000819910.1 link	n.68-4889T>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.137

AC:

20791

AN:

151990

Hom.:

2118

Cov.:

show subpopulations

Gnomad AFR

AF:

0.280

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.0786

Gnomad ASJ

AF:

0.0900

Gnomad EAS

AF:

0.0410

Gnomad SAS

AF:

0.160

Gnomad FIN

AF:

0.118

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.0757

Gnomad OTH

AF:

0.136

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

GnomAD4 genome

AF:

0.137

AC:

20825

AN:

152108

Hom.:

2121

Cov.:

AF XY:

0.140

AC XY:

10395

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.280

AC:

11596

AN:

41450

American (AMR)

AF:

0.0785

AC:

1200

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0900

AC:

312

AN:

3468

East Asian (EAS)

AF:

0.0413

AC:

214

AN:

5184

South Asian (SAS)

AF:

0.160

AC:

769

AN:

4818

European-Finnish (FIN)

AF:

0.118

AC:

1247

AN:

10588

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0757

AC:

5146

AN:

67996

Other (OTH)

AF:

0.135

AC:

284

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

871

1742

2612

3483

4354

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

222

444

666

888

1110

<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:

0.0935

Hom.:

1907

Bravo

AF:

0.139

Asia WGS

AF:

0.106

AC:

368

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

5.0

(source)

DANN

Benign

0.22

PhyloP100

0.19

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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