11-113323114-A-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_017868.4(TTC12):c.59-174A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0649 in 151,540 control chromosomes in the GnomAD database, including 490 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.065 (490 hom., cov: 31)
• Consequence: TTC12 NM_017868.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.319

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 11-113323114-A-C is Benign according to our data. Variant chr11-113323114-A-C is described in ClinVar as [Benign]. Clinvar id is 1250113.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC12	NM_017868.4	c.59-174A>C		intron_variant		ENST00000529221.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC12	ENST00000529221.6	c.59-174A>C		intron_variant		2	NM_017868.4	A2

Frequencies

GnomAD3 genomes AF: 0.0650 AC: 9841 AN: 151426 Hom.: 490 Cov.: 31

Gnomad AFR AF: 0.0174

Gnomad AMI AF: 0.0738

Gnomad AMR AF: 0.0302

Gnomad ASJ AF: 0.0900

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.00582

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0992

Gnomad OTH AF: 0.0533

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

GnomAD4 genome AF: 0.0649 AC: 9842 AN: 151540 Hom.: 490 Cov.: 31 AF XY: 0.0641 AC XY: 4742 AN XY: 73980

Gnomad4 AFR AF: 0.0174

Gnomad4 AMR AF: 0.0300

Gnomad4 ASJ AF: 0.0900

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.00604

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.0992

Gnomad4 OTH AF: 0.0527

Alfa AF: 0.0866 Hom.: 111

Bravo AF: 0.0550

Asia WGS AF: 0.00809 AC: 29 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.40
Dann	Benign	0.41

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: rs55939425; hg19: chr11-113193836;