rs4648356

chr1-2792599-C-A

Variant summary

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

The NM_001242672.3(TTC34):c.785-2253G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,994 control chromosomes in the GnomAD database, including 11,960 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 0.39 (11960 hom., cov: 31)
• Consequence: TTC34 NM_001242672.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC34	NM_001242672.3	c.785-2253G>T		intron_variant		ENST00000401095.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC34	ENST00000401095.9	c.785-2253G>T		intron_variant		5	NM_001242672.3	P1

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58759 AN: 151878 Hom.: 11943 Cov.: 31

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.387 AC: 58802 AN: 151994 Hom.: 11960 Cov.: 31 AF XY: 0.392 AC XY: 29119 AN XY: 74274

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.359

Alfa AF: 0.339 Hom.: 4326

Bravo AF: 0.391

Asia WGS AF: 0.573 AC: 1995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.1
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4648356; hg19: chr1-2709164;