rs17817077

Positions:

• chr18-74542308-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

CNDP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNDP1	NM_032649.6	c.24+7617G>A		intron_variant		ENST00000358821.8	NP_116038.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNDP1	ENST00000358821.8	c.24+7617G>A		intron_variant		1	NM_032649.6	ENSP00000351682.3
CNDP1	ENST00000582365.1	c.24+7617G>A		intron_variant		5		ENSP00000462096.1
CNDP1	ENST00000585136.1	n.189+7617G>A		intron_variant		3

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

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.0889

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.315

Alfa AF: 0.380 Hom.: 15005

Bravo AF: 0.283

Asia WGS AF: 0.212 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.28

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: rs17817077; hg19: chr18-72209543;