rs159695

chr12-29580833-C-Achr12-29580833-C-Gchr12-29580833-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001193451.2(TMTC1):c.1418+2574G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,528 control chromosomes in the GnomAD database, including 26,646 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 0.58 (26646 hom., cov: 31)
• Consequence: TMTC1 NM_001193451.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315

Genes affected

TMTC1 (HGNC:24099): (transmembrane O-mannosyltransferase targeting cadherins 1) Enables mannosyltransferase activity. Involved in protein O-linked mannosylation. Predicted to be located in endoplasmic reticulum. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMTC1	NM_001193451.2	c.1418+2574G>T		intron_variant		ENST00000539277.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMTC1	ENST00000539277.6	c.1418+2574G>T		intron_variant		1	NM_001193451.2

Frequencies

GnomAD3 genomes AF: 0.580 AC: 87805 AN: 151410 Hom.: 26646 Cov.: 31

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.580 AC: 87812 AN: 151528 Hom.: 26646 Cov.: 31 AF XY: 0.580 AC XY: 42873 AN XY: 73974

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.595

Alfa AF: 0.637 Hom.: 12272

Bravo AF: 0.574

Asia WGS AF: 0.573 AC: 1995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.23
Dann	Benign	0.40

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: rs159695; hg19: chr12-29733766;