rs7927508

chr11-113317475-G-Achr11-113317475-G-Cchr11-113317475-G-T

Variant summary

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

The NM_017868.4(TTC12):c.58+1160G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 151,464 control chromosomes in the GnomAD database, including 28,550 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 0.61 (28550 hom., cov: 29)
• Consequence: TTC12 NM_017868.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67

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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC12	NM_017868.4	c.58+1160G>A		intron_variant		ENST00000529221.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC12	ENST00000529221.6	c.58+1160G>A		intron_variant		2	NM_017868.4	A2

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92516 AN: 151346 Hom.: 28544 Cov.: 29

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.611 AC: 92562 AN: 151464 Hom.: 28550 Cov.: 29 AF XY: 0.605 AC XY: 44763 AN XY: 73976

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.615

Alfa AF: 0.613 Hom.: 11636

Bravo AF: 0.616

Asia WGS AF: 0.585 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.0050
Dann	Benign	0.19

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: rs7927508; hg19: chr11-113188197;