rs1055076

chr11-113368987-C-A

Variant summary

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

The ENST00000314756.7(TTC12):c.*120+524C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 158,828 control chromosomes in the GnomAD database, including 4,464 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 0.22 (4336 hom., cov: 32)
  • Exomes 𝑓: 0.17 (128 hom.)
• Consequence: TTC12 ENST00000314756.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC12	NR_165393.1	n.2267C>A		non_coding_transcript_exon_variant	17/17
TTC12	NR_147891.2	n.2370+524C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000602900.1	n.510C>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32918 AN: 151916 Hom.: 4327 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.196

GnomAD4 exome AF: 0.170 AC: 1155 AN: 6794 Hom.: 128 Cov.: 0 AF XY: 0.170 AC XY: 601 AN XY: 3526

Gnomad4 AFR exome AF: 0.259

Gnomad4 AMR exome AF: 0.198

Gnomad4 ASJ exome AF: 0.179

Gnomad4 EAS exome AF: 0.497

Gnomad4 SAS exome AF: 0.186

Gnomad4 FIN exome AF: 0.132

Gnomad4 NFE exome AF: 0.130

Gnomad4 OTH exome AF: 0.152

GnomAD4 genome AF: 0.217 AC: 32955 AN: 152034 Hom.: 4336 Cov.: 32 AF XY: 0.224 AC XY: 16618 AN XY: 74312

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.195

Alfa AF: 0.150 Hom.: 1942

Bravo AF: 0.220

Asia WGS AF: 0.332 AC: 1153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.33
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1055076; hg19: chr11-113239709;