Genetic Variant NM_019026.6:c.469-141_469-140delAA (chr1-165728260-CTT-C) – ACMG Classification: Uncertain_significance (2 pts)

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]

TMCO1 links:

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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	Effect	Exon rank	MANE	Protein	UniProt
TMCO1	NM_019026.6 link	c.469-141_469-140delAA	intron_variant	Intron 6 of 6	ENST00000367881.11	NP_061899.3	Q9UM00-1
TMCO1	NM_001256164.1 link	c.520-141_520-140delAA	intron_variant	Intron 6 of 6		NP_001243093.1	B7Z591
TMCO1	NM_001256165.1 link	c.433-141_433-140delAA	intron_variant	Intron 6 of 6		NP_001243094.1	B7Z591
TMCO1	NR_045818.1 link	n.563-141_563-140delAA	intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMCO1	ENST00000367881.11 link	c.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:

AN:

144188

Hom.:

Cov.:

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.:

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:

AN:

144238

Hom.:

Cov.:

AF XY:

0.000114

AC XY:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over