GeneBe

rs55850117

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_153704.6(TMEM67):​c.*19T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

TMEM67
NM_153704.6 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0280

Publications

0 publications found
Variant links:
Genes affected
TMEM67 (HGNC:28396): (transmembrane protein 67) The protein encoded by this gene localizes to the primary cilium and to the plasma membrane. The gene functions in centriole migration to the apical membrane and formation of the primary cilium. Multiple transcript variants encoding different isoforms have been found for this gene. Defects in this gene are a cause of Meckel syndrome type 3 (MKS3) and Joubert syndrome type 6 (JBTS6). [provided by RefSeq, Nov 2008]
TMEM67 Gene-Disease associations (from GenCC):
  • ciliopathy
    Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
  • COACH syndrome 1
    Inheritance: AR Classification: DEFINITIVE Submitted by: G2P
  • Meckel syndrome, type 3
    Inheritance: AR Classification: DEFINITIVE Submitted by: Ambry Genetics
  • nephronophthisis 11
    Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P
  • COACH syndrome 1
    Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics
  • Joubert syndrome 6
    Inheritance: AR Classification: STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
  • Joubert syndrome
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • Meckel syndrome
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • Senior-Boichis syndrome
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TMEM67NM_153704.6 linkc.*19T>A 3_prime_UTR_variant Exon 28 of 28 ENST00000453321.8 NP_714915.3 Q5HYA8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TMEM67ENST00000453321.8 linkc.*19T>A 3_prime_UTR_variant Exon 28 of 28 1 NM_153704.6 ENSP00000389998.3 Q5HYA8

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1290038
Hom.:
0
Cov.:
18
AF XY:
0.00
AC XY:
0
AN XY:
650502
African (AFR)
AF:
0.00
AC:
0
AN:
29958
American (AMR)
AF:
0.00
AC:
0
AN:
43758
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
24866
East Asian (EAS)
AF:
0.00
AC:
0
AN:
38674
South Asian (SAS)
AF:
0.00
AC:
0
AN:
80894
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53038
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5372
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
959068
Other (OTH)
AF:
0.00
AC:
0
AN:
54410
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
6.8
DANN
Benign
0.79
PhyloP100
0.028

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: rs55850117; hg19: chr8-94828699; API