1-230954832-G-C

Variant names:

• chr1-230954832-G-C
• rs6541240
• NM_024525.5:c.443-429C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_024525.5(TTC13):​c.443-429C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: TTC13 NM_024525.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.866
• Publications: 5 publications found

Genes affected

TTC13 (HGNC:26204): (tetratricopeptide repeat domain 13)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024525.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC13	NM_024525.5	MANE Select	c.443-429C>G		intron	N/A	NP_078801.3
	TTC13	NM_001376510.1		c.443-429C>G		intron	N/A	NP_001363439.1
	TTC13	NM_001376507.1		c.443-429C>G		intron	N/A	NP_001363436.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC13	ENST00000366661.9	TSL:1 MANE Select	c.443-429C>G		intron	N/A	ENSP00000355621.4
	TTC13	ENST00000366662.8	TSL:1	c.443-429C>G		intron	N/A	ENSP00000355622.4
	TTC13	ENST00000522821.5	TSL:4	c.407-429C>G		intron	N/A	ENSP00000430385.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.40
DANN	Benign	0.49
PhyloP100		-0.87

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: rs6541240; hg19: chr1-231090578;