dbSNP rs1055076: TTC12:c.*120+524C>A (chr11-113368987-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.143

Variant links:

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 links:

ENSG00000270179 (HGNC:):

ENSG00000270179 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 rank	MANE	Protein	UniProt
TTC12	NR_165393.1 link	n.2267C>A		non_coding_transcript_exon_variant	Exon 17 of 17
TTC12	NR_147891.2 link	n.2370+524C>A		intron_variant	Intron 22 of 22

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
TTC12	ENST00000314756.7 link	c.*120+524C>A	intron_variant	Intron 21 of 21	1	ENSP00000315160.3	Q9H892-2
TTC12	ENST00000494714.5 link	n.*120+524C>A	intron_variant	Intron 22 of 22	1	ENSP00000435291.1	Q9H892-2
TTC12	ENST00000393020.5 link	c.1968+411C>A	intron_variant	Intron 21 of 21	5	ENSP00000376743.1	A8MTE9

Frequencies

GnomAD3 genomes

AF:

0.217

AC:

32918

AN:

151916

Hom.:

4327

Cov.:

show subpopulations

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.:

AF XY:

0.170

AC XY:

601

AN XY:

3526

show subpopulations

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.:

AF XY:

0.224

AC XY:

16618

AN XY:

74312

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over