NM_019026.6:c.469-141_469-140delAA

Variant summary

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

The NM_019026.6(TMCO1):​c.469-141_469-140delAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00315 in 454,156 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000069 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0046 ( 0 hom. )

Consequence

TMCO1
NM_019026.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.355
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]

Genome browser will be placed here

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.469-141_469-140delAA intron_variant Intron 6 of 6 ENST00000367881.11 NP_061899.3 Q9UM00-1
TMCO1NM_001256164.1 linkc.520-141_520-140delAA intron_variant Intron 6 of 6 NP_001243093.1 B7Z591
TMCO1NM_001256165.1 linkc.433-141_433-140delAA intron_variant Intron 6 of 6 NP_001243094.1 B7Z591
TMCO1NR_045818.1 linkn.563-141_563-140delAA intron_variant Intron 6 of 6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TMCO1ENST00000367881.11 linkc.469-141_469-140delAA intron_variant Intron 6 of 6 1 NM_019026.6 ENSP00000356856.6 Q9UM00-1

Frequencies

GnomAD3 genomes
AF:
0.0000624
AC:
9
AN:
144188
Hom.:
0
Cov.:
31
show subpopulations
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:
0.000338
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000918
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00458
AC:
1419
AN:
309918
Hom.:
0
AF XY:
0.00460
AC XY:
795
AN XY:
172788
show subpopulations
Gnomad4 AFR exome
AF:
0.00348
Gnomad4 AMR exome
AF:
0.00648
Gnomad4 ASJ exome
AF:
0.00628
Gnomad4 EAS exome
AF:
0.00342
Gnomad4 SAS exome
AF:
0.00343
Gnomad4 FIN exome
AF:
0.00405
Gnomad4 NFE exome
AF:
0.00476
Gnomad4 OTH exome
AF:
0.00476
GnomAD4 genome
AF:
0.0000693
AC:
10
AN:
144238
Hom.:
0
Cov.:
31
AF XY:
0.000114
AC XY:
8
AN XY:
69972
show subpopulations
Gnomad4 AFR
AF:
0.0000252
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000338
Gnomad4 NFE
AF:
0.0000918
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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

LitVar

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

Other links and lift over

dbSNP: rs397967679; hg19: chr1-165697497; API