2-201628160-TAAA-TAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001044385.3(TMEM237):​c.870-12_870-11insTT variant causes a splice polypyrimidine tract, intron change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)

Consequence

TMEM237
NM_001044385.3 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.95
Variant links:
Genes affected
TMEM237 (HGNC:14432): (transmembrane protein 237) The protein encoded by this gene is a tetraspanin protein that is thought to be involved in WNT signaling. Defects in this gene are a cause of Joubert syndrome-14. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TMEM237NM_001044385.3 linkuse as main transcriptc.870-12_870-11insTT splice_polypyrimidine_tract_variant, intron_variant ENST00000409883.7 NP_001037850.1
TMEM237NM_152388.4 linkuse as main transcriptc.846-12_846-11insTT splice_polypyrimidine_tract_variant, intron_variant NP_689601.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TMEM237ENST00000409883.7 linkuse as main transcriptc.870-12_870-11insTT splice_polypyrimidine_tract_variant, intron_variant 5 NM_001044385.3 ENSP00000386264 P4Q96Q45-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
26
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-202492883; API