rs890337

Variant names:

• chr18-74518737-G-A
• rs890337
• NM_018235.3:c.1210+97G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CNDP2	NM_018235.3	c.1210+97G>A		intron_variant	Intron 10 of 11	ENST00000324262.9	NP_060705.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNDP2	ENST00000324262.9	c.1210+97G>A		intron_variant	Intron 10 of 11	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

African (AFR) AF: 0.751 AC: 23852 AN: 31744

American (AMR) AF: 0.972 AC: 42362 AN: 43572

Ashkenazi Jewish (ASJ) AF: 0.995 AC: 24248 AN: 24376

East Asian (EAS) AF: 0.892 AC: 34822 AN: 39048

South Asian (SAS) AF: 0.948 AC: 77170 AN: 81398

European-Finnish (FIN) AF: 0.993 AC: 49077 AN: 49436

Middle Eastern (MID) AF: 0.967 AC: 4265 AN: 4412

European-Non Finnish (NFE) AF: 0.982 AC: 1025676 AN: 1044628

Other (OTH) AF: 0.956 AC: 54825 AN: 57366

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

African (AFR) AF: 0.753 AC: 31232 AN: 41476

American (AMR) AF: 0.945 AC: 14463 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.997 AC: 3458 AN: 3470

East Asian (EAS) AF: 0.886 AC: 4569 AN: 5154

South Asian (SAS) AF: 0.952 AC: 4597 AN: 4830

European-Finnish (FIN) AF: 0.994 AC: 10562 AN: 10628

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.983 AC: 66844 AN: 68034

Other (OTH) AF: 0.929 AC: 1966 AN: 2116

Alfa AF: 0.936 Hom.: 26013

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
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs890337; hg19: chr18-72185972;