rs7170952

chr15-99210240-A-G

Variant summary

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

The NM_001288615.3(TTC23):c.581+8348T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0902 in 152,160 control chromosomes in the GnomAD database, including 1,001 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 0.090 (1001 hom., cov: 32)
• Consequence: TTC23 NM_001288615.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.742

Genes affected

TTC23 (HGNC:25730): (tetratricopeptide repeat domain 23) Predicted to be involved in positive regulation of smoothened signaling pathway. Predicted to be located in cilium. [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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC23	NM_001288615.3	c.581+8348T>C		intron_variant		ENST00000394132.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC23	ENST00000394132.7	c.581+8348T>C		intron_variant		1	NM_001288615.3	P1

Frequencies

GnomAD3 genomes AF: 0.0902 AC: 13718 AN: 152044 Hom.: 1001 Cov.: 32

Gnomad AFR AF: 0.0211

Gnomad AMI AF: 0.0606

Gnomad AMR AF: 0.0951

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0857

Gnomad OTH AF: 0.0976

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

GnomAD4 genome AF: 0.0902 AC: 13731 AN: 152160 Hom.: 1001 Cov.: 32 AF XY: 0.0982 AC XY: 7308 AN XY: 74388

Gnomad4 AFR AF: 0.0211

Gnomad4 AMR AF: 0.0955

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.0857

Gnomad4 OTH AF: 0.0990

Alfa AF: 0.0804 Hom.: 110

Bravo AF: 0.0776

Asia WGS AF: 0.226 AC: 788 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.51
Dann	Benign	0.76

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: rs7170952; hg19: chr15-99750445;