rs2377041

Positions:

• chr1-2796762-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.784+3282G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,008 control chromosomes in the GnomAD database, including 10,608 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 0.36 (10608 hom., cov: 32)
• Consequence: TTC34 NM_001242672.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TTC34	NM_001242672.3	c.784+3282G>A		intron_variant		ENST00000401095.9	NP_001229601.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TTC34	ENST00000401095.9	c.784+3282G>A		intron_variant		5	NM_001242672.3	ENSP00000383873	P1

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54256 AN: 151888 Hom.: 10595 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.357 AC: 54301 AN: 152008 Hom.: 10608 Cov.: 32 AF XY: 0.354 AC XY: 26280 AN XY: 74266

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.399

Alfa AF: 0.433 Hom.: 23909

Bravo AF: 0.357

Asia WGS AF: 0.270 AC: 937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2377041; hg19: chr1-2713327;