NM_032649.6:c.89C>A

Variant names:

• chr18-74556402-C-A
• rs559481897
• NM_032649.6:c.89C>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_032649.6(CNDP1):​c.89C>A​(p.Pro30Gln) 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. 15/20 in silico tools predict 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. P30L) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: CNDP1 NM_032649.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 0 publications found

Genes affected

CNDP1 (HGNC:20675): (carnosine dipeptidase 1) This gene encodes a member of the M20 metalloprotease family. The encoded protein is specifically expressed in the brain, is a homodimeric dipeptidase which was identified as human carnosinase. This gene contains trinucleotide (CTG) repeat length polymorphism in the coding region. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.068481356).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032649.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP1	NM_032649.6	MANE Select	c.89C>A	p.Pro30Gln	missense	Exon 2 of 12	NP_116038.4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP1	ENST00000358821.8	TSL:1 MANE Select	c.89C>A	p.Pro30Gln	missense	Exon 2 of 12	ENSP00000351682.3	Q96KN2
	CNDP1	ENST00000864762.1		c.89C>A	p.Pro30Gln	missense	Exon 2 of 12	ENSP00000534821.1
	CNDP1	ENST00000954332.1		c.89C>A	p.Pro30Gln	missense	Exon 2 of 12	ENSP00000624391.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.090
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.64
CADD	Benign	7.0
DANN	Benign	0.90
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.084	N
M_CAP	Benign	0.0055	T
MetaRNN	Benign	0.068	T
MetaSVM	Benign	-0.99	T
PhyloP100		0.12
PrimateAI	Benign	0.28	T
PROVEAN	Benign	-0.71	N
REVEL	Benign	0.024
Sift	Uncertain	0.0070	D
Sift4G	Benign	0.097	T
Vest4		0.35
MutPred		0.26		Loss of glycosylation at P30 (P = 0.0064)
MVP		0.048
MPC		0.28
ClinPred		0.26	T
GERP RS		0.86
gMVP		0.27
Mutation Taster		=97/3	polymorphism

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

Other links and lift over

dbSNP: rs559481897; hg19: chr18-72223637;