11-113323102-C-CA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_017868.4(TTC12):c.59-167dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 79,196 control chromosomes in the GnomAD database, including 1,861 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.27 (1861 hom., cov: 23)
• Consequence: TTC12 NM_017868.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.19

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 -10 ACMG points.

• BP6: Variant 11-113323102-C-CA is Benign according to our data. Variant chr11-113323102-C-CA is described in ClinVar as [Benign]. Clinvar id is 1270524.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC12	NM_017868.4	c.59-167dup		intron_variant		ENST00000529221.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC12	ENST00000529221.6	c.59-167dup		intron_variant		2	NM_017868.4	A2

Frequencies

GnomAD3 genomes AF: 0.269 AC: 21266 AN: 79190 Hom.: 1864 Cov.: 23

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.268 AC: 21253 AN: 79196 Hom.: 1861 Cov.: 23 AF XY: 0.266 AC XY: 9857 AN XY: 37054

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.275

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

Jun 04, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs34496236; hg19: chr11-113193824;