Variant chr11-113323254-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_017868.4(TTC12):c.59-34T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.017 in 1,497,306 control chromosomes in the GnomAD database, including 313 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.012 ( 19 hom., cov: 32)

Exomes 𝑓: 0.018 ( 294 hom. )

Consequence

TTC12
NM_017868.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.275

Variant links:

Genes affected

TTC12 (HGNC:23700): (tetratricopeptide repeat domain 12) Involved in axonemal dynein complex assembly and sperm axoneme assembly. Located in centrosome and cytoplasm. Implicated in primary ciliary dyskinesia 45. [provided by Alliance of Genome Resources, Apr 2022]

TTC12 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 11-113323254-T-C is Benign according to our data. Variant chr11-113323254-T-C is described in ClinVar as [Benign]. Clinvar id is 1265170.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.053 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC12	NM_017868.4 linkuse as main transcript	c.59-34T>C		intron_variant		ENST00000529221.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC12	ENST00000529221.6 linkuse as main transcript	c.59-34T>C		intron_variant		2	NM_017868.4	A2	Q9H892-1

Frequencies

GnomAD3 genomes

AF:

0.0116

AC:

1768

AN:

152144

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00287

Gnomad AMI

AF:

0.0252

Gnomad AMR

AF:

0.00792

Gnomad ASJ

AF:

0.00836

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.0536

Gnomad FIN

AF:

0.00745

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0162

Gnomad OTH

AF:

0.0163

GnomAD3 exomes

AF:

0.0163

AC:

3104

AN:

191010

Hom.:

AF XY:

0.0187

AC XY:

1933

AN XY:

103354

show subpopulations

Gnomad AFR exome

AF:

0.00225

Gnomad AMR exome

AF:

0.00761

Gnomad ASJ exome

AF:

0.0108

Gnomad EAS exome

AF:

0.000137

Gnomad SAS exome

AF:

0.0535

Gnomad FIN exome

AF:

0.00872

Gnomad NFE exome

AF:

0.0172

Gnomad OTH exome

AF:

0.0170

GnomAD4 exome

AF:

0.0176

AC:

23672

AN:

1345044

Hom.:

294

Cov.:

AF XY:

0.0184

AC XY:

12272

AN XY:

665424

show subpopulations

Gnomad4 AFR exome

AF:

0.00206

Gnomad4 AMR exome

AF:

0.00844

Gnomad4 ASJ exome

AF:

0.0100

Gnomad4 EAS exome

AF:

0.0000808

Gnomad4 SAS exome

AF:

0.0545

Gnomad4 FIN exome

AF:

0.00920

Gnomad4 NFE exome

AF:

0.0172

Gnomad4 OTH exome

AF:

0.0166

GnomAD4 genome

AF:

0.0116

AC:

1773

AN:

152262

Hom.:

Cov.:

AF XY:

0.0122

AC XY:

908

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.00286

Gnomad4 AMR

AF:

0.00791

Gnomad4 ASJ

AF:

0.00836

Gnomad4 EAS

AF:

0.000387

Gnomad4 SAS

AF:

0.0547

Gnomad4 FIN

AF:

0.00745

Gnomad4 NFE

AF:

0.0162

Gnomad4 OTH

AF:

0.0161

Alfa

AF:

0.0124

Hom.:

Bravo

AF:

0.0104

Asia WGS

AF:

0.0140

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 17, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.0

DANN

Benign

0.72

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over