rs7170952

Variant names:

• chr15-99210240-A-G
• rs7170952
• NM_001288615.3:c.581+8348T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TTC23	NM_001288615.3	c.581+8348T>C		intron_variant	Intron 8 of 13	ENST00000394132.7	NP_001275544.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTC23	ENST00000394132.7	c.581+8348T>C		intron_variant	Intron 8 of 13	1	NM_001288615.3	ENSP00000377690.2

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

African (AFR) AF: 0.0211 AC: 877 AN: 41528

American (AMR) AF: 0.0955 AC: 1461 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 608 AN: 3466

East Asian (EAS) AF: 0.310 AC: 1607 AN: 5182

South Asian (SAS) AF: 0.179 AC: 865 AN: 4822

European-Finnish (FIN) AF: 0.208 AC: 2195 AN: 10566

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0857 AC: 5827 AN: 67998

Other (OTH) AF: 0.0990 AC: 208 AN: 2102

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
PhyloP100		-0.74
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: rs7170952; hg19: chr15-99750445;