rs10502173

chr11-113332301-C-Achr11-113332301-C-T

Variant summary

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

The NM_017868.4(TTC12):c.504+2322C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,044 control chromosomes in the GnomAD database, including 5,243 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 0.24 (5243 hom., cov: 32)
• Consequence: TTC12 NM_017868.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC12	NM_017868.4	c.504+2322C>A		intron_variant		ENST00000529221.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC12	ENST00000529221.6	c.504+2322C>A		intron_variant		2	NM_017868.4	A2

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36205 AN: 151926 Hom.: 5226 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.238 AC: 36262 AN: 152044 Hom.: 5243 Cov.: 32 AF XY: 0.243 AC XY: 18079 AN XY: 74320

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.221

Alfa AF: 0.150 Hom.: 1054

Bravo AF: 0.244

Asia WGS AF: 0.356 AC: 1238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.0
Dann	Benign	0.56

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: rs10502173; hg19: chr11-113203023;