rs4891562

chr18-74567102-A-Cchr18-74567102-A-G

Variant summary

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

The NM_032649.6(CNDP1):c.556-131A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 694,244 control chromosomes in the GnomAD database, including 132,748 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 0.56 (25158 hom., cov: 31)
  • Exomes 𝑓: 0.62 (107590 hom.)
• Consequence: CNDP1 NM_032649.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.02

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=-1.08).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNDP1	NM_032649.6	c.556-131A>C		intron_variant		ENST00000358821.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNDP1	ENST00000358821.8	c.556-131A>C		intron_variant		1	NM_032649.6	P1
CNDP1	ENST00000582365.1	c.427-131A>C		intron_variant		5
CNDP1	ENST00000584316.5	c.*24-131A>C		intron_variant, NMD_transcript_variant		4
CNDP1	ENST00000585136.1	n.558-131A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85030 AN: 151904 Hom.: 25152 Cov.: 31

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.590

GnomAD4 exome AF: 0.622 AC: 337219 AN: 542222 Hom.: 107590 AF XY: 0.619 AC XY: 179004 AN XY: 289094

Gnomad4 AFR exome AF: 0.357

Gnomad4 AMR exome AF: 0.576

Gnomad4 ASJ exome AF: 0.639

Gnomad4 EAS exome AF: 0.363

Gnomad4 SAS exome AF: 0.539

Gnomad4 FIN exome AF: 0.667

Gnomad4 NFE exome AF: 0.671

Gnomad4 OTH exome AF: 0.612

GnomAD4 genome AF: 0.559 AC: 85051 AN: 152022 Hom.: 25158 Cov.: 31 AF XY: 0.557 AC XY: 41399 AN XY: 74330

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.589

Alfa AF: 0.496 Hom.: 1523

Bravo AF: 0.546

Asia WGS AF: 0.460 AC: 1598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.034
Dann	Benign	0.11

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: rs4891562; hg19: chr18-72234337; COSMIC: COSV62594867; COSMIC: COSV62594867;