rs4648499

chr1-2783104-C-Achr1-2783104-C-Gchr1-2783104-C-T

Variant summary

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

The NM_001242672.3(TTC34):c.2226+505G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,164 control chromosomes in the GnomAD database, including 2,910 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 0.19 (2910 hom., cov: 33)
• Consequence: TTC34 NM_001242672.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

Genes affected

TTC34 (HGNC:34297): (tetratricopeptide repeat domain 34)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC34	NM_001242672.3	c.2226+505G>T		intron_variant		ENST00000401095.9
LOC105378598	XR_007065372.1	n.2992-1244C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC34	ENST00000401095.9	c.2226+505G>T		intron_variant		5	NM_001242672.3	P1
	ENST00000648684.1	n.208-1244C>A		intron_variant, non_coding_transcript_variant
TTC34	ENST00000637179.1	c.687+505G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28356 AN: 152046 Hom.: 2913 Cov.: 33

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.0770

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.186 AC: 28367 AN: 152164 Hom.: 2910 Cov.: 33 AF XY: 0.186 AC XY: 13815 AN XY: 74398

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.0772

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.193

Alfa AF: 0.201 Hom.: 1800

Bravo AF: 0.176

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.022

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4648499; hg19: chr1-2699649;