11-113379003-G-C

Position:

• chr11-113379003-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000393020.5(TTC12):​c.1969-4374G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 152,110 control chromosomes in the GnomAD database, including 35,614 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.68 (35614 hom., cov: 32)
• Consequence: TTC12 ENST00000393020.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TTC12	ENST00000393020.5	c.1969-4374G>C		intron_variant		5		ENSP00000376743

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103396 AN: 151992 Hom.: 35597 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.680 AC: 103458 AN: 152110 Hom.: 35614 Cov.: 32 AF XY: 0.676 AC XY: 50270 AN XY: 74342

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.682

Alfa AF: 0.585 Hom.: 1836

Bravo AF: 0.677

Asia WGS AF: 0.555 AC: 1927 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.081
DANN	Benign	0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3897584; hg19: chr11-113249725;