1-165766938-C-T

Position:

• chr1-165766938-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMCO1	NM_019026.6	c.148+1254G>A		intron_variant		ENST00000367881.11	NP_061899.3
TMCO1	NM_001256164.1	c.199+1254G>A		intron_variant			NP_001243093.1
TMCO1	NM_001256165.1	c.112+1254G>A		intron_variant			NP_001243094.1
TMCO1	NR_045818.1	n.242+1254G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMCO1	ENST00000367881.11	c.148+1254G>A		intron_variant		1	NM_019026.6	ENSP00000356856.6

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

Gnomad4 AFR AF: 0.928

Gnomad4 AMR AF: 0.879

Gnomad4 ASJ AF: 0.926

Gnomad4 EAS AF: 0.991

Gnomad4 SAS AF: 0.938

Gnomad4 FIN AF: 0.819

Gnomad4 NFE AF: 0.877

Gnomad4 OTH AF: 0.897

Alfa AF: 0.866 Hom.: 4872

Bravo AF: 0.899

Asia WGS AF: 0.960 AC: 3338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.63

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

Other links and lift over

dbSNP: rs4657477; hg19: chr1-165736175;