NM_032256.3:c.768+29254G>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_032256.3(TMEM117):​c.768+29254G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 27)
Failed GnomAD Quality Control

Consequence

TMEM117
NM_032256.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.262

Publications

3 publications found
Variant links:
Genes affected
TMEM117 (HGNC:25308): (transmembrane protein 117) Involved in intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress. Located in endoplasmic reticulum and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TMEM117NM_032256.3 linkc.768+29254G>T intron_variant Intron 6 of 7 ENST00000266534.8 NP_115632.1 Q9H0C3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TMEM117ENST00000266534.8 linkc.768+29254G>T intron_variant Intron 6 of 7 1 NM_032256.3 ENSP00000266534.3 Q9H0C3

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
151104
Hom.:
0
Cov.:
27
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
151104
Hom.:
0
Cov.:
27
AF XY:
0.00
AC XY:
0
AN XY:
73672
African (AFR)
AF:
0.00
AC:
0
AN:
41136
American (AMR)
AF:
0.00
AC:
0
AN:
15104
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3466
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5098
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4752
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10414
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
314
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
67832
Other (OTH)
AF:
0.00
AC:
0
AN:
2082

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.96
DANN
Benign
0.46
PhyloP100
-0.26

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs1726886; hg19: chr12-44722776; API