rs9807352

Positions:

• chr18-74559343-C-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The ENST00000358821.8(CNDP1):​c.174C>A​(p.Ala58=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0321 in 1,613,966 control chromosomes in the GnomAD database, including 1,441 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 0.058 (474 hom., cov: 32)
  • Exomes 𝑓: 0.029 (967 hom.)
• Consequence: CNDP1 ENST00000358821.8 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.71

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

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BP7: Synonymous conserved (PhyloP=-4.71 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNDP1	NM_032649.6	c.174C>A	p.Ala58=	synonymous_variant	3/12	ENST00000358821.8	NP_116038.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNDP1	ENST00000358821.8	c.174C>A	p.Ala58=	synonymous_variant	3/12	1	NM_032649.6	ENSP00000351682	P1
CNDP1	ENST00000582365.1	c.45C>A	p.Ala15=	synonymous_variant	2/11	5		ENSP00000462096
CNDP1	ENST00000585136.1	n.339C>A		non_coding_transcript_exon_variant	3/5	3

Frequencies

GnomAD3 genomes AF: 0.0584 AC: 8885 AN: 152086 Hom.: 472 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0344

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.0661

Gnomad SAS AF: 0.0257

Gnomad FIN AF: 0.0200

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0267

Gnomad OTH AF: 0.0556

GnomAD3 exomes AF: 0.0346 AC: 8691 AN: 251306 Hom.: 287 AF XY: 0.0324 AC XY: 4403 AN XY: 135838

Gnomad AFR exome AF: 0.144

Gnomad AMR exome AF: 0.0183

Gnomad ASJ exome AF: 0.0192

Gnomad EAS exome AF: 0.0640

Gnomad SAS exome AF: 0.0220

Gnomad FIN exome AF: 0.0240

Gnomad NFE exome AF: 0.0262

Gnomad OTH exome AF: 0.0302

GnomAD4 exome AF: 0.0294 AC: 42959 AN: 1461762 Hom.: 967 Cov.: 34 AF XY: 0.0290 AC XY: 21058 AN XY: 727184

Gnomad4 AFR exome AF: 0.148

Gnomad4 AMR exome AF: 0.0205

Gnomad4 ASJ exome AF: 0.0191

Gnomad4 EAS exome AF: 0.0596

Gnomad4 SAS exome AF: 0.0230

Gnomad4 FIN exome AF: 0.0256

Gnomad4 NFE exome AF: 0.0256

Gnomad4 OTH exome AF: 0.0360

GnomAD4 genome AF: 0.0584 AC: 8895 AN: 152204 Hom.: 474 Cov.: 32 AF XY: 0.0578 AC XY: 4300 AN XY: 74410

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0343

Gnomad4 ASJ AF: 0.0167

Gnomad4 EAS AF: 0.0657

Gnomad4 SAS AF: 0.0257

Gnomad4 FIN AF: 0.0200

Gnomad4 NFE AF: 0.0267

Gnomad4 OTH AF: 0.0550

Alfa AF: 0.0337 Hom.: 203

Bravo AF: 0.0645

Asia WGS AF: 0.0450 AC: 156 AN: 3478

EpiCase AF: 0.0267

EpiControl AF: 0.0235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	1.7
DANN	Benign	0.80

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: rs9807352; hg19: chr18-72226578; COSMIC: COSV62593816; COSMIC: COSV62593816;