18-74496224-A-T

Position:

• chr18-74496224-A-T

Variant summary

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

The ENST00000581272.5(CNDP2):​c.-38+301A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 152,052 control chromosomes in the GnomAD database, including 46,630 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 0.78 (46599 hom., cov: 32)
  • Exomes 𝑓: 0.78 (31 hom.)
• Consequence: CNDP2 ENST00000581272.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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=-1.12).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNDP2	ENST00000581272.5	c.-38+301A>T		intron_variant		4		ENSP00000464151
CNDP2	ENST00000580672.5			upstream_gene_variant		5		ENSP00000464214

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118672 AN: 151846 Hom.: 46571 Cov.: 32

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.771

GnomAD4 exome AF: 0.784 AC: 69 AN: 88 Hom.: 31 Cov.: 0 AF XY: 0.750 AC XY: 48 AN XY: 64

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.667

Gnomad4 NFE exome AF: 0.782

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.781 AC: 118749 AN: 151964 Hom.: 46599 Cov.: 32 AF XY: 0.782 AC XY: 58113 AN XY: 74310

Gnomad4 AFR AF: 0.792

Gnomad4 AMR AF: 0.829

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.957

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.774

Alfa AF: 0.769 Hom.: 5289

Bravo AF: 0.790

Asia WGS AF: 0.885 AC: 3076 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	3.6
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		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: rs6566810; hg19: chr18-72163459;