chr1-2641891-G-C

Variant names:

• chr1-2641891-G-C
• rs772710901
• NM_001242672.3:c.2717C>G

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001242672.3(TTC34):​c.2717C>G​(p.Ala906Gly) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A906V) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 34)
• Consequence: TTC34 NM_001242672.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.62
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.41748753).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTC34	NM_001242672.3	c.2717C>G	p.Ala906Gly	missense_variant	Exon 9 of 9	ENST00000401095.9	NP_001229601.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTC34	ENST00000401095.9	c.2717C>G	p.Ala906Gly	missense_variant	Exon 9 of 9	5	NM_001242672.3	ENSP00000383873.4
TTC34	ENST00000637179.1	c.1178C>G	p.Ala393Gly	missense_variant	Exon 7 of 7	5		ENSP00000490537.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.25
BayesDel_addAF	Benign	-0.10	T
BayesDel_noAF	Benign	-0.38
CADD	Uncertain	24
DANN	Benign	0.96
DEOGEN2	Benign	0.38	.;T
Eigen	Benign	-0.0059
Eigen_PC	Benign	-0.094
FATHMM_MKL	Benign	0.68	D
LIST_S2	Benign	0.62	T;.
M_CAP	Uncertain	0.11	D
MetaRNN	Benign	0.42	T;T
MetaSVM	Benign	-0.86	T
MutationAssessor	Pathogenic	3.0	.;M
PhyloP100		3.6
PrimateAI	Uncertain	0.50	T
REVEL	Benign	0.17
MutPred		0.55		.;Loss of stability (P = 0.0998);
MVP		0.17
ClinPred		0.73	D
GERP RS		3.4
Varity_R		0.14
gMVP		0.22
Mutation Taster		=74/26	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs772710901; hg19: chr1-2573330;