3-33114416-G-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_006371.5(CRTAP):​c.339G>T​(p.Leu113Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000715 in 1,397,910 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 34)
Exomes 𝑓: 7.2e-7 ( 0 hom. )

Consequence

CRTAP
NM_006371.5 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.96
Variant links:
Genes affected
CRTAP (HGNC:2379): (cartilage associated protein) The protein encoded by this gene is similar to the chicken and mouse CRTAP genes. The encoded protein is a scaffolding protein that may influence the activity of at least one member of the cytohesin/ARNO family in response to specific cellular stimuli. Defects in this gene are associated with osteogenesis imperfecta, a connective tissue disorder characterized by bone fragility and low bone mass. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP7
Synonymous conserved (PhyloP=2.96 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CRTAPNM_006371.5 linkuse as main transcriptc.339G>T p.Leu113Leu synonymous_variant 1/7 ENST00000320954.11 NP_006362.1 O75718
CRTAPNM_001393363.1 linkuse as main transcriptc.339G>T p.Leu113Leu synonymous_variant 1/6 NP_001380292.1
CRTAPNM_001393364.1 linkuse as main transcriptc.339G>T p.Leu113Leu synonymous_variant 1/6 NP_001380293.1
CRTAPNM_001393365.1 linkuse as main transcriptc.339G>T p.Leu113Leu synonymous_variant 1/6 NP_001380294.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CRTAPENST00000320954.11 linkuse as main transcriptc.339G>T p.Leu113Leu synonymous_variant 1/71 NM_006371.5 ENSP00000323696.5 O75718
CRTAPENST00000449224.1 linkuse as main transcriptc.339G>T p.Leu113Leu synonymous_variant 1/62 ENSP00000409997.1 C9JP16

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
AF:
7.15e-7
AC:
1
AN:
1397910
Hom.:
0
Cov.:
32
AF XY:
0.00000145
AC XY:
1
AN XY:
691166
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000278
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.55
CADD
Benign
13
DANN
Benign
0.82
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs960380634; hg19: chr3-33155908; API