rs2346064

chr18-74546181-T-C

Variant summary

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

The NM_032649.6(CNDP1):c.25-10157T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 152,134 control chromosomes in the GnomAD database, including 12,401 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 0.39 (12401 hom., cov: 32)
• Consequence: CNDP1 NM_032649.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNDP1	NM_032649.6	c.25-10157T>C		intron_variant		ENST00000358821.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNDP1	ENST00000358821.8	c.25-10157T>C		intron_variant		1	NM_032649.6	P1
CNDP1	ENST00000582365.1	c.24+11490T>C		intron_variant		5
CNDP1	ENST00000585136.1	n.190-10157T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58864 AN: 152016 Hom.: 12382 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.387 AC: 58929 AN: 152134 Hom.: 12401 Cov.: 32 AF XY: 0.388 AC XY: 28859 AN XY: 74360

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.416

Alfa AF: 0.338 Hom.: 12888

Bravo AF: 0.399

Asia WGS AF: 0.279 AC: 968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.5
Dann	Benign	0.44

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: rs2346064; hg19: chr18-72213416;