rs2377041

Variant names:

• chr1-2796762-C-T
• rs2377041
• NM_001242672.3:c.784+3282G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TTC34	NM_001242672.3	c.784+3282G>A		intron_variant	Intron 2 of 8	ENST00000401095.9	NP_001229601.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTC34	ENST00000401095.9	c.784+3282G>A		intron_variant	Intron 2 of 8	5	NM_001242672.3	ENSP00000383873.4

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

African (AFR) AF: 0.189 AC: 7818 AN: 41468

American (AMR) AF: 0.402 AC: 6138 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1699 AN: 3472

East Asian (EAS) AF: 0.371 AC: 1911 AN: 5154

South Asian (SAS) AF: 0.252 AC: 1210 AN: 4810

European-Finnish (FIN) AF: 0.398 AC: 4195 AN: 10538

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29945 AN: 67964

Other (OTH) AF: 0.399 AC: 842 AN: 2110

Alfa AF: 0.419 Hom.: 52703

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
PhyloP100		-0.049
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2377041; hg19: chr1-2713327;