rs4846884

Positions:

• chr1-230951329-A-C
• chr1-230951329-A-G
• chr1-230951329-A-T

Variant summary

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

The NM_024525.5(TTC13):​c.513+3004T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.857 in 151,830 control chromosomes in the GnomAD database, including 55,779 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 0.86 (55779 hom., cov: 29)
• Consequence: TTC13 NM_024525.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

Genes affected

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

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 = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC13	NM_024525.5	c.513+3004T>G		intron_variant		ENST00000366661.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC13	ENST00000366661.9	c.513+3004T>G		intron_variant		1	NM_024525.5	P1

Frequencies

GnomAD3 genomes AF: 0.857 AC: 130010 AN: 151714 Hom.: 55740 Cov.: 29

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.857 AC: 130106 AN: 151830 Hom.: 55779 Cov.: 29 AF XY: 0.859 AC XY: 63737 AN XY: 74212

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.822

Gnomad4 EAS AF: 0.978

Gnomad4 SAS AF: 0.851

Gnomad4 FIN AF: 0.902

Gnomad4 NFE AF: 0.859

Gnomad4 OTH AF: 0.831

Alfa AF: 0.850 Hom.: 69541

Bravo AF: 0.855

Asia WGS AF: 0.887 AC: 3081 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	8.8
DANN	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs4846884; hg19: chr1-231087075;