NM_017868.4:c.58+1160G>A

Variant names:

• chr11-113317475-G-A
• rs7927508
• NM_017868.4:c.58+1160G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

TTC12 Gene-Disease associations (from GenCC):

• ciliary dyskinesia, primary, 45

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
• primary ciliary dyskinesia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TTC12	NM_017868.4	c.58+1160G>A		intron_variant	Intron 2 of 21	ENST00000529221.6	NP_060338.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTC12	ENST00000529221.6	c.58+1160G>A		intron_variant	Intron 2 of 21	2	NM_017868.4	ENSP00000433757.1

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

African (AFR) AF: 0.618 AC: 25466 AN: 41212

American (AMR) AF: 0.589 AC: 8974 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2195 AN: 3460

East Asian (EAS) AF: 0.481 AC: 2464 AN: 5126

South Asian (SAS) AF: 0.609 AC: 2922 AN: 4798

European-Finnish (FIN) AF: 0.534 AC: 5600 AN: 10478

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 42959 AN: 67852

Other (OTH) AF: 0.615 AC: 1295 AN: 2106

Alfa AF: 0.614 Hom.: 13319

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
PhyloP100		-2.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7927508; hg19: chr11-113188197;