Variant 11-113323597-AT-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_017868.4(TTC12):c.222+156del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 514,116 control chromosomes in the GnomAD database, including 6,850 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.14 ( 1883 hom., cov: 29)

Exomes 𝑓: 0.16 ( 4967 hom. )

Consequence

TTC12
NM_017868.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.983

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 -10 ACMG points.

BP6

Variant 11-113323597-AT-A is Benign according to our data. Variant chr11-113323597-AT-A is described in ClinVar as [Benign]. Clinvar id is 1220837.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TTC12	NM_017868.4 linkuse as main transcript	c.222+156del		intron_variant		ENST00000529221.6	NP_060338.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TTC12	ENST00000529221.6 linkuse as main transcript	c.222+156del		intron_variant		2	NM_017868.4	ENSP00000433757	A2	Q9H892-1

Frequencies

GnomAD3 genomes

AF:

0.143

AC:

21465

AN:

150392

Hom.:

1885

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0369

Gnomad AMI

AF:

0.282

Gnomad AMR

AF:

0.122

Gnomad ASJ

AF:

0.181

Gnomad EAS

AF:

0.0766

Gnomad SAS

AF:

0.223

Gnomad FIN

AF:

0.176

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.201

Gnomad OTH

AF:

0.150

GnomAD4 exome

AF:

0.159

AC:

57834

AN:

363614

Hom.:

4967

AF XY:

0.161

AC XY:

29752

AN XY:

184332

show subpopulations

Gnomad4 AFR exome

AF:

0.0316

Gnomad4 AMR exome

AF:

0.121

Gnomad4 ASJ exome

AF:

0.190

Gnomad4 EAS exome

AF:

0.0822

Gnomad4 SAS exome

AF:

0.202

Gnomad4 FIN exome

AF:

0.176

Gnomad4 NFE exome

AF:

0.168

Gnomad4 OTH exome

AF:

0.155

GnomAD4 genome

AF:

0.143

AC:

21457

AN:

150502

Hom.:

1883

Cov.:

AF XY:

0.142

AC XY:

10461

AN XY:

73470

show subpopulations

Gnomad4 AFR

AF:

0.0368

Gnomad4 AMR

AF:

0.122

Gnomad4 ASJ

AF:

0.181

Gnomad4 EAS

AF:

0.0764

Gnomad4 SAS

AF:

0.223

Gnomad4 FIN

AF:

0.176

Gnomad4 NFE

AF:

0.201

Gnomad4 OTH

AF:

0.152

Bravo

AF:

0.129

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 17, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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