rs17817077

Variant names:

• chr18-74542308-G-A
• rs17817077
• NM_032649.6:c.24+7617G>A

Variant summary

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

The NM_032649.6(CNDP1):​c.24+7617G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,200 control chromosomes in the GnomAD database, including 7,757 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 0.30 (7757 hom., cov: 33)
• Consequence: CNDP1 NM_032649.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.394 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP1	NM_032649.6	MANE Select	c.24+7617G>A		intron	N/A	NP_116038.4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP1	ENST00000358821.8	TSL:1 MANE Select	c.24+7617G>A		intron	N/A	ENSP00000351682.3	Q96KN2
	CNDP1	ENST00000864762.1		c.24+7617G>A		intron	N/A	ENSP00000534821.1
	CNDP1	ENST00000954332.1		c.24+7617G>A		intron	N/A	ENSP00000624391.1

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45119 AN: 152082 Hom.: 7762 Cov.: 33

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.0895

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.296 AC: 45116 AN: 152200 Hom.: 7757 Cov.: 33 AF XY: 0.295 AC XY: 21960 AN XY: 74412

African (AFR) AF: 0.136 AC: 5638 AN: 41546

American (AMR) AF: 0.263 AC: 4023 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1290 AN: 3472

East Asian (EAS) AF: 0.0889 AC: 460 AN: 5172

South Asian (SAS) AF: 0.378 AC: 1822 AN: 4820

European-Finnish (FIN) AF: 0.338 AC: 3578 AN: 10592

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27073 AN: 67978

Other (OTH) AF: 0.315 AC: 666 AN: 2116

Alfa AF: 0.366 Hom.: 19760

Bravo AF: 0.283

Asia WGS AF: 0.212 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.28
PhyloP100		0.15
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: rs17817077; hg19: chr18-72209543;