chr1-2783104-C-A

Variant names:

• chr1-2783104-C-A
• rs4648499
• NM_001242672.3:c.2226+505G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

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

ENSG00000285945 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001242672.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC34	NM_001242672.3	MANE Select	c.2226+505G>T		intron	N/A	NP_001229601.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC34	ENST00000401095.9	TSL:5 MANE Select	c.2226+505G>T		intron	N/A	ENSP00000383873.4
	TTC34	ENST00000637179.1	TSL:5	c.687+505G>T		intron	N/A	ENSP00000490537.1
	ENSG00000285945	ENST00000648684.1		n.208-1244C>A		intron	N/A

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

African (AFR) AF: 0.140 AC: 5811 AN: 41508

American (AMR) AF: 0.130 AC: 1981 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 681 AN: 3472

East Asian (EAS) AF: 0.0772 AC: 400 AN: 5180

South Asian (SAS) AF: 0.256 AC: 1236 AN: 4824

European-Finnish (FIN) AF: 0.215 AC: 2278 AN: 10578

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15152 AN: 67996

Other (OTH) AF: 0.193 AC: 409 AN: 2114

Alfa AF: 0.200 Hom.: 2521

Bravo AF: 0.176

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.022
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs4648499; hg19: chr1-2699649;