17-78997112-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001159773.2(CANT1):​c.511A>C​(p.Ile171Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

CANT1
NM_001159773.2 missense

Scores

1
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.781
Variant links:
Genes affected
CANT1 (HGNC:19721): (calcium activated nucleotidase 1) This protein encoded by this gene belongs to the apyrase family. It functions as a calcium-dependent nucleotidase with a preference for UDP. Mutations in this gene are associated with Desbuquois dysplasia with hand anomalies. Alternatively spliced transcript variants have been noted for this gene.[provided by RefSeq, Mar 2010]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.18952775).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CANT1NM_001159773.2 linkuse as main transcriptc.511A>C p.Ile171Leu missense_variant 3/5 ENST00000392446.10 NP_001153245.1
CANT1NM_001159772.2 linkuse as main transcriptc.511A>C p.Ile171Leu missense_variant 4/6 NP_001153244.1
CANT1NM_138793.4 linkuse as main transcriptc.511A>C p.Ile171Leu missense_variant 2/4 NP_620148.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CANT1ENST00000392446.10 linkuse as main transcriptc.511A>C p.Ile171Leu missense_variant 3/51 NM_001159773.2 ENSP00000376241 P1Q8WVQ1-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.26
T
BayesDel_noAF
Benign
-0.26
CADD
Benign
13
DANN
Benign
0.95
DEOGEN2
Benign
0.32
T
Eigen
Benign
-0.89
Eigen_PC
Benign
-0.90
FATHMM_MKL
Uncertain
0.77
D
LIST_S2
Benign
0.15
T
M_CAP
Benign
0.0086
T
MetaRNN
Benign
0.19
T
MutationTaster
Benign
0.99
D;D;D
MVP
0.48
ClinPred
0.18
T
GERP RS
-4.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1014317450; hg19: chr17-76993194; API