1-165766938-C-T

Variant names:

• chr1-165766938-C-T
• rs4657477
• NM_019026.6:c.148+1254G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019026.6(TMCO1):​c.148+1254G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 152,124 control chromosomes in the GnomAD database, including 61,002 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.89 (61002 hom., cov: 30)
• Consequence: TMCO1 NM_019026.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 11 publications found

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 Gene-Disease associations (from GenCC):

• cerebrofaciothoracic dysplasia

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, Laboratory for Molecular Medicine, Orphanet, PanelApp Australia, Illumina
• craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development 1

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019026.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMCO1	NM_019026.6	MANE Select	c.148+1254G>A		intron	N/A	NP_061899.3
	TMCO1	NM_001256164.1		c.199+1254G>A		intron	N/A	NP_001243093.1
	TMCO1	NM_001256165.1		c.112+1254G>A		intron	N/A	NP_001243094.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMCO1	ENST00000367881.11	TSL:1 MANE Select	c.148+1254G>A		intron	N/A	ENSP00000356856.6
	TMCO1	ENST00000612311.4	TSL:1	c.301+1254G>A		intron	N/A	ENSP00000480514.1
	TMCO1	ENST00000868463.1		c.148+1254G>A		intron	N/A	ENSP00000538522.1

Frequencies

GnomAD3 genomes AF: 0.895 AC: 135981 AN: 152006 Hom.: 60940 Cov.: 30

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.926

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.938

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.896

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.895 AC: 136102 AN: 152124 Hom.: 61002 Cov.: 30 AF XY: 0.894 AC XY: 66494 AN XY: 74356

African (AFR) AF: 0.928 AC: 38506 AN: 41514

American (AMR) AF: 0.879 AC: 13427 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.926 AC: 3209 AN: 3466

East Asian (EAS) AF: 0.991 AC: 5135 AN: 5182

South Asian (SAS) AF: 0.938 AC: 4526 AN: 4824

European-Finnish (FIN) AF: 0.819 AC: 8632 AN: 10538

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.877 AC: 59664 AN: 67998

Other (OTH) AF: 0.897 AC: 1897 AN: 2114

Alfa AF: 0.868 Hom.: 5188

Bravo AF: 0.899

Asia WGS AF: 0.960 AC: 3338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.63
PhyloP100		-0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4657477; hg19: chr1-165736175;