rs41307798

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_007272.3(CTRC):​c.285C>A​(p.Asp95Glu) 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. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. D95D) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)

Consequence

CTRC
NM_007272.3 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -6.81
Variant links:
Genes affected
CTRC (HGNC:2523): (chymotrypsin C) This gene encodes a member of the peptidase S1 family. The encoded protein is a serum calcium-decreasing factor that has chymotrypsin-like protease activity. Alternatively spliced transcript variants have been observed, but their full-length nature has not been determined. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.051425695).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CTRCNM_007272.3 linkc.285C>A p.Asp95Glu missense_variant Exon 4 of 8 ENST00000375949.5 NP_009203.2 Q99895
CTRCXM_011540550.2 linkc.285C>A p.Asp95Glu missense_variant Exon 4 of 7 XP_011538852.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CTRCENST00000375949.5 linkc.285C>A p.Asp95Glu missense_variant Exon 4 of 8 1 NM_007272.3 ENSP00000365116.4 Q99895
CTRCENST00000375943.6 linkc.95C>A p.Thr32Lys missense_variant Exon 2 of 5 1 ENSP00000365110.2 Q68DR9
CTRCENST00000476813.5 linkn.107C>A non_coding_transcript_exon_variant Exon 2 of 3 3
CTRCENST00000483406.1 linkn.195C>A non_coding_transcript_exon_variant Exon 3 of 6 5

Frequencies

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
-0.14
T
BayesDel_noAF
Benign
-0.44
CADD
Benign
0.0020
DANN
Benign
0.45
DEOGEN2
Benign
0.13
T
Eigen
Benign
-1.4
Eigen_PC
Benign
-1.6
FATHMM_MKL
Benign
0.044
N
LIST_S2
Benign
0.55
T
M_CAP
Benign
0.027
D
MetaRNN
Benign
0.051
T
MetaSVM
Benign
-0.92
T
MutationAssessor
Benign
0.21
N
PrimateAI
Benign
0.33
T
PROVEAN
Benign
-0.50
N
REVEL
Benign
0.25
Sift
Benign
1.0
T
Sift4G
Benign
0.75
T
Polyphen
0.0
B
Vest4
0.19
MutPred
0.35
Gain of disorder (P = 0.1132);
MVP
0.58
MPC
0.17
ClinPred
0.032
T
GERP RS
-6.2
Varity_R
0.14
gMVP
0.49

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-15768997; API