rs17089362

chr18-74518403-G-Achr18-74518403-G-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_018235.3(CNDP2):c.1069-96G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00104 in 1,434,144 control chromosomes in the GnomAD database, including 1 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 0.0020 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00093 (1 hom.)
• Consequence: CNDP2 NM_018235.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNDP2	NM_018235.3	c.1069-96G>A		intron_variant		ENST00000324262.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNDP2	ENST00000324262.9	c.1069-96G>A		intron_variant		1	NM_018235.3	P1

Frequencies

GnomAD3 genomes AF: 0.00199 AC: 303 AN: 152164 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00418

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00301

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.000705

Gnomad OTH AF: 0.00335

GnomAD4 exome AF: 0.000929 AC: 1191 AN: 1281862 Hom.: 1 Cov.: 18 AF XY: 0.000933 AC XY: 597 AN XY: 639744

Gnomad4 AFR exome AF: 0.00434

Gnomad4 AMR exome AF: 0.00317

Gnomad4 ASJ exome AF: 0.00709

Gnomad4 EAS exome AF: 0.00171

Gnomad4 SAS exome AF: 0.000131

Gnomad4 FIN exome AF: 0.000184

Gnomad4 NFE exome AF: 0.000577

Gnomad4 OTH exome AF: 0.00204

GnomAD4 genome AF: 0.00200 AC: 304 AN: 152282 Hom.: 0 Cov.: 33 AF XY: 0.00212 AC XY: 158 AN XY: 74468

Gnomad4 AFR AF: 0.00419

Gnomad4 AMR AF: 0.00301

Gnomad4 ASJ AF: 0.00576

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000706

Gnomad4 OTH AF: 0.00331

Alfa AF: 0.00000676 Hom.: 45

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.0010
Dann	Benign	0.59

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: rs17089362; hg19: chr18-72185638;