chr18-74551466-C-T

Variant names:

• chr18-74551466-C-T
• rs17089382
• NM_032649.6:c.25-4872C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032649.6(CNDP1):​c.25-4872C>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
• Publications: 8 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP1	NM_032649.6	MANE Select	c.25-4872C>T		intron	N/A	NP_116038.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP1	ENST00000358821.8	TSL:1 MANE Select	c.25-4872C>T		intron	N/A	ENSP00000351682.3
	CNDP1	ENST00000582365.1	TSL:5	c.25-7857C>T		intron	N/A	ENSP00000462096.1
	CNDP1	ENST00000585136.1	TSL:3	n.190-4872C>T		intron	N/A

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

African (AFR) AF: 0.193 AC: 7976 AN: 41316

American (AMR) AF: 0.166 AC: 2536 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 538 AN: 3472

East Asian (EAS) AF: 0.0966 AC: 499 AN: 5166

South Asian (SAS) AF: 0.125 AC: 602 AN: 4810

European-Finnish (FIN) AF: 0.155 AC: 1629 AN: 10522

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7432 AN: 67954

Other (OTH) AF: 0.160 AC: 338 AN: 2112

Alfa AF: 0.121 Hom.: 2468

Bravo AF: 0.146

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.7
DANN	Benign	0.67
PhyloP100		0.044
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: rs17089382; hg19: chr18-72218701;