rs890337

Positions:

• chr18-74518737-G-A

Variant summary

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

The NM_018235.3(CNDP2):​c.1210+97G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.965 in 1,528,196 control chromosomes in the GnomAD database, including 714,188 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 0.91 (64107 hom., cov: 33)
  • Exomes 𝑓: 0.97 (650081 hom.)
• Consequence: CNDP2 NM_018235.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

CNDP2 (HGNC:24437): (carnosine dipeptidase 2) CNDP2, also known as tissue carnosinase and peptidase A (EC 3.4.13.18), is a nonspecific dipeptidase rather than a selective carnosinase (Teufel et al., 2003 [PubMed 12473676]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNDP2	NM_018235.3	c.1210+97G>A		intron_variant		ENST00000324262.9	NP_060705.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNDP2	ENST00000324262.9	c.1210+97G>A		intron_variant		1	NM_018235.3	ENSP00000325548.4

Frequencies

GnomAD3 genomes AF: 0.912 AC: 138772 AN: 152098 Hom.: 64098 Cov.: 33

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.945

Gnomad ASJ AF: 0.997

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.994

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.983

Gnomad OTH AF: 0.930

GnomAD4 exome AF: 0.971 AC: 1336297 AN: 1375980 Hom.: 650081 Cov.: 21 AF XY: 0.971 AC XY: 665997 AN XY: 685726

Gnomad4 AFR exome AF: 0.751

Gnomad4 AMR exome AF: 0.972

Gnomad4 ASJ exome AF: 0.995

Gnomad4 EAS exome AF: 0.892

Gnomad4 SAS exome AF: 0.948

Gnomad4 FIN exome AF: 0.993

Gnomad4 NFE exome AF: 0.982

Gnomad4 OTH exome AF: 0.956

GnomAD4 genome AF: 0.912 AC: 138810 AN: 152216 Hom.: 64107 Cov.: 33 AF XY: 0.915 AC XY: 68089 AN XY: 74428

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.945

Gnomad4 ASJ AF: 0.997

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.952

Gnomad4 FIN AF: 0.994

Gnomad4 NFE AF: 0.983

Gnomad4 OTH AF: 0.929

Alfa AF: 0.942 Hom.: 13113

Bravo AF: 0.902

Asia WGS AF: 0.917 AC: 3191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs890337; hg19: chr18-72185972;