18-24102336-C-T

Position:

• chr18-24102336-C-T

Variant summary

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

The NM_001135993.2(TTC39C):​c.985-12218C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,068 control chromosomes in the GnomAD database, including 5,449 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 (5449 hom., cov: 33)
• Consequence: TTC39C NM_001135993.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

TTC39C (HGNC:26595): (tetratricopeptide repeat domain 39C) Predicted to be involved in cilium assembly and otolith morphogenesis. [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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TTC39C	NM_001135993.2	c.985-12218C>T		intron_variant		ENST00000317571.8	NP_001129465.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TTC39C	ENST00000317571.8	c.985-12218C>T		intron_variant		1	NM_001135993.2	ENSP00000323645.3
TTC39C	ENST00000304621.10	c.802-12218C>T		intron_variant		1		ENSP00000306598.6

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35834 AN: 151950 Hom.: 5442 Cov.: 33

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.236 AC: 35890 AN: 152068 Hom.: 5449 Cov.: 33 AF XY: 0.238 AC XY: 17665 AN XY: 74352

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.230

Alfa AF: 0.123 Hom.: 384

Bravo AF: 0.245

Asia WGS AF: 0.254 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.46
DANN	Benign	0.82

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: rs16940484; hg19: chr18-21682300;