NM_032649.6:c.25-10157T>C

Variant names:

• chr18-74546181-T-C
• rs2346064
• NM_032649.6:c.25-10157T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
CNDP1	NM_032649.6	c.25-10157T>C		intron_variant	Intron 1 of 11	ENST00000358821.8	NP_116038.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNDP1	ENST00000358821.8	c.25-10157T>C		intron_variant	Intron 1 of 11	1	NM_032649.6	ENSP00000351682.3
CNDP1	ENST00000582365.1	c.24+11490T>C		intron_variant	Intron 1 of 10	5		ENSP00000462096.1
CNDP1	ENST00000585136.1	n.190-10157T>C		intron_variant	Intron 1 of 4	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

African (AFR) AF: 0.557 AC: 23111 AN: 41484

American (AMR) AF: 0.376 AC: 5747 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1261 AN: 3470

East Asian (EAS) AF: 0.140 AC: 725 AN: 5182

South Asian (SAS) AF: 0.359 AC: 1732 AN: 4820

European-Finnish (FIN) AF: 0.334 AC: 3528 AN: 10570

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21422 AN: 67998

Other (OTH) AF: 0.416 AC: 877 AN: 2110

Alfa AF: 0.345 Hom.: 18365

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
PhyloP100		-0.43
Mutation Taster		=100/0	polymorphism (auto)

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: rs2346064; hg19: chr18-72213416;