NM_018235.3:c.1069-96G>A

Variant names:

• chr18-74518403-G-A
• rs17089362
• NM_018235.3:c.1069-96G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. 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
• Publications: 3 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNDP2	NM_018235.3	c.1069-96G>A		intron_variant	Intron 9 of 11	ENST00000324262.9	NP_060705.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNDP2	ENST00000324262.9	c.1069-96G>A		intron_variant	Intron 9 of 11	1	NM_018235.3	ENSP00000325548.4

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

African (AFR) AF: 0.00434 AC: 130 AN: 29934

American (AMR) AF: 0.00317 AC: 132 AN: 41584

Ashkenazi Jewish (ASJ) AF: 0.00709 AC: 160 AN: 22564

East Asian (EAS) AF: 0.00171 AC: 66 AN: 38498

South Asian (SAS) AF: 0.000131 AC: 10 AN: 76238

European-Finnish (FIN) AF: 0.000184 AC: 9 AN: 48818

Middle Eastern (MID) AF: 0.00326 AC: 17 AN: 5220

European-Non Finnish (NFE) AF: 0.000577 AC: 557 AN: 965070

Other (OTH) AF: 0.00204 AC: 110 AN: 53936

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

African (AFR) AF: 0.00419 AC: 174 AN: 41538

American (AMR) AF: 0.00301 AC: 46 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00576 AC: 20 AN: 3472

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5180

South Asian (SAS) AF: 0.00 AC: 0 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10614

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.000706 AC: 48 AN: 68036

Other (OTH) AF: 0.00331 AC: 7 AN: 2112

Alfa AF: 0.00000458 Hom.: 134

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
PhyloP100		-2.2
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs17089362; hg19: chr18-72185638;