18-74521017-A-G

Variant names:

• chr18-74521017-A-G
• rs890335
• NM_018235.3:c.*949A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018235.3(CNDP2):​c.*949A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.954 in 152,198 control chromosomes in the GnomAD database, including 69,615 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 0.95 (69610 hom., cov: 32)
  • Exomes 𝑓: 1.0 (5 hom.)
• Consequence: CNDP2 NM_018235.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018235.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP2	NM_018235.3	MANE Select	c.*949A>G		3_prime_UTR	Exon 12 of 12	NP_060705.2	Q96KP4-1
	CNDP2	NM_001370248.1		c.*949A>G		3_prime_UTR	Exon 12 of 12	NP_001357177.1	Q96KP4-1
	CNDP2	NM_001370249.1		c.*949A>G		3_prime_UTR	Exon 14 of 14	NP_001357178.1	Q96KP4-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP2	ENST00000324262.9	TSL:1 MANE Select	c.*949A>G		3_prime_UTR	Exon 12 of 12	ENSP00000325548.4	Q96KP4-1
	CNDP2	ENST00000324301.12	TSL:1	c.*949A>G		3_prime_UTR	Exon 9 of 9	ENSP00000325756.8	Q96KP4-2
	CNDP2	ENST00000880651.1		c.*949A>G		3_prime_UTR	Exon 12 of 12	ENSP00000550710.1

Frequencies

GnomAD3 genomes AF: 0.954 AC: 145101 AN: 152070 Hom.: 69568 Cov.: 32

Gnomad AFR AF: 0.855

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.978

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.902

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.964

GnomAD4 exome AF: 1.00 AC: 10 AN: 10 Hom.: 5 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 4 AN: 4

Other (OTH) AF: 1.00 AC: 4 AN: 4

GnomAD4 genome AF: 0.954 AC: 145201 AN: 152188 Hom.: 69610 Cov.: 32 AF XY: 0.955 AC XY: 71052 AN XY: 74428

African (AFR) AF: 0.855 AC: 35462 AN: 41482

American (AMR) AF: 0.978 AC: 14957 AN: 15292

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 0.902 AC: 4645 AN: 5150

South Asian (SAS) AF: 1.00 AC: 4824 AN: 4826

European-Finnish (FIN) AF: 1.00 AC: 10615 AN: 10616

Middle Eastern (MID) AF: 0.997 AC: 293 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67987 AN: 68030

Other (OTH) AF: 0.962 AC: 2034 AN: 2114

Alfa AF: 0.983 Hom.: 24840

Bravo AF: 0.948

Asia WGS AF: 0.956 AC: 3323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.28
PhyloP100		-0.028
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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: rs890335; hg19: chr18-72188252;