Variant chr11-113316157-C-T 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.-15-86C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 528,770 control chromosomes in the GnomAD database, including 22,109 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 5269 hom., cov: 33)

Exomes 𝑓: 0.29 ( 16840 hom. )

Consequence

TTC12
NM_017868.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.03

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=-0.57).

BP6

Variant 11-113316157-C-T is Benign according to our data. Variant chr11-113316157-C-T is described in ClinVar as [Benign]. Clinvar id is 1253908.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.327 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.-15-86C>T		intron_variant		ENST00000529221.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC12	ENST00000529221.6 linkuse as main transcript	c.-15-86C>T		intron_variant		2	NM_017868.4	A2	Q9H892-1

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37361

AN:

151964

Hom.:

5269

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.224

Gnomad AMR

AF:

0.315

Gnomad ASJ

AF:

0.350

Gnomad EAS

AF:

0.341

Gnomad SAS

AF:

0.254

Gnomad FIN

AF:

0.272

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.298

Gnomad OTH

AF:

0.261

GnomAD4 exome

AF:

0.295

AC:

111021

AN:

376688

Hom.:

16840

Cov.:

AF XY:

0.295

AC XY:

56300

AN XY:

191078

show subpopulations

Gnomad4 AFR exome

AF:

0.0998

Gnomad4 AMR exome

AF:

0.334

Gnomad4 ASJ exome

AF:

0.336

Gnomad4 EAS exome

AF:

0.300

Gnomad4 SAS exome

AF:

0.260

Gnomad4 FIN exome

AF:

0.260

Gnomad4 NFE exome

AF:

0.306

Gnomad4 OTH exome

AF:

0.288

GnomAD4 genome

AF:

0.246

AC:

37357

AN:

152082

Hom.:

5269

Cov.:

AF XY:

0.246

AC XY:

18284

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.106

Gnomad4 AMR

AF:

0.315

Gnomad4 ASJ

AF:

0.350

Gnomad4 EAS

AF:

0.340

Gnomad4 SAS

AF:

0.254

Gnomad4 FIN

AF:

0.272

Gnomad4 NFE

AF:

0.298

Gnomad4 OTH

AF:

0.259

Alfa

AF:

0.262

Hom.:

896

Bravo

AF:

0.248

Asia WGS

AF:

0.299

AC:

1038

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

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

DANN

Benign

0.62

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