GeneBe

1-165743318-GAAA-GAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Variant names:

Variant summary

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

The NM_019026.6(TMCO1):​c.324-8_324-7insTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 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

TMCO1
NM_019026.6 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.01
Variant links:
Genes affected
TMCO1 (HGNC:18188): (transmembrane and coiled-coil domains 1) This locus encodes a transmembrane protein. Mutations at this locus have been associated with craniofacial dysmorphism, skeletal anomalies, and cognitive disability. Mutations at this locus have also been associated with open angle glaucoma blindness. Alternatively spliced transcript variants have been described. [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 rank MANE Protein UniProt
TMCO1NM_019026.6 linkc.324-8_324-7insTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT splice_region_variant, intron_variant Intron 5 of 6 ENST00000367881.11 NP_061899.3 Q9UM00-1
TMCO1NM_001256164.1 linkc.375-8_375-7insTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT splice_region_variant, intron_variant Intron 5 of 6 NP_001243093.1 B7Z591
TMCO1NM_001256165.1 linkc.288-8_288-7insTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT splice_region_variant, intron_variant Intron 5 of 6 NP_001243094.1 B7Z591
TMCO1NR_045818.1 linkn.418-8_418-7insTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT splice_region_variant, intron_variant Intron 5 of 6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TMCO1ENST00000367881.11 linkc.324-8_324-7insTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT splice_region_variant, intron_variant Intron 5 of 6 1 NM_019026.6 ENSP00000356856.6 Q9UM00-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
0
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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs751227407; hg19: chr1-165712555; API