rs17089382

Positions:

• chr18-74551466-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032649.6(CNDP1):​c.25-4872C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 151,794 control chromosomes in the GnomAD database, including 1,689 homozygotes. 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: 𝑓 0.14 (1689 hom., cov: 31)
• Consequence: CNDP1 NM_032649.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440

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]

CNDP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNDP1	NM_032649.6	c.25-4872C>T		intron_variant		ENST00000358821.8	NP_116038.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNDP1	ENST00000358821.8	c.25-4872C>T		intron_variant		1	NM_032649.6	ENSP00000351682.3
CNDP1	ENST00000582365.1	c.25-7857C>T		intron_variant		5		ENSP00000462096.1
CNDP1	ENST00000585136.1	n.190-4872C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21624 AN: 151676 Hom.: 1687 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0964

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.159

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.143 AC: 21651 AN: 151794 Hom.: 1689 Cov.: 31 AF XY: 0.143 AC XY: 10647 AN XY: 74196

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.0966

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.160

Alfa AF: 0.119 Hom.: 1539

Bravo AF: 0.146

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.7
DANN	Benign	0.67

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

Other links and lift over

dbSNP: rs17089382; hg19: chr18-72218701;