rs751227407

Variant summary

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

The NM_019026.6(TMCO1):​c.324-10_324-8delTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000684 in 1,345,488 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000010 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000073 ( 0 hom. )

Consequence

TMCO1
NM_019026.6 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.54
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.324-10_324-8delTTT splice_region_variant, intron_variant Intron 5 of 6 ENST00000367881.11 NP_061899.3 Q9UM00-1
TMCO1NM_001256164.1 linkc.375-10_375-8delTTT splice_region_variant, intron_variant Intron 5 of 6 NP_001243093.1 B7Z591
TMCO1NM_001256165.1 linkc.288-10_288-8delTTT splice_region_variant, intron_variant Intron 5 of 6 NP_001243094.1 B7Z591
TMCO1NR_045818.1 linkn.418-10_418-8delTTT 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.324-10_324-8delTTT splice_region_variant, intron_variant Intron 5 of 6 1 NM_019026.6 ENSP00000356856.6 Q9UM00-1

Frequencies

GnomAD3 genomes
AF:
0.0000105
AC:
1
AN:
95686
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:
0.000173
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000728
AC:
91
AN:
1249802
Hom.:
0
AF XY:
0.0000527
AC XY:
33
AN XY:
625696
show subpopulations
Gnomad4 AFR exome
AF:
0.000108
Gnomad4 AMR exome
AF:
0.000162
Gnomad4 ASJ exome
AF:
0.0000436
Gnomad4 EAS exome
AF:
0.0000279
Gnomad4 SAS exome
AF:
0.0000399
Gnomad4 FIN exome
AF:
0.000333
Gnomad4 NFE exome
AF:
0.0000581
Gnomad4 OTH exome
AF:
0.0000959
GnomAD4 genome
AF:
0.0000105
AC:
1
AN:
95686
Hom.:
0
Cov.:
31
AF XY:
0.0000218
AC XY:
1
AN XY:
45864
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000173
Gnomad4 NFE
AF:
0.00
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: rs751227407; hg19: chr1-165712555; API