18-74521112-T-C

Variant names:

• chr18-74521112-T-C
• rs7577
• NM_018235.3:c.*1044T>C

Variant summary

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

The NM_018235.3(CNDP2):​c.*1044T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,198 control chromosomes in the GnomAD database, including 4,089 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 0.21 (4089 hom., cov: 33)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: CNDP2 NM_018235.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 24 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 = 0.29 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP2	NM_018235.3	MANE Select	c.*1044T>C		3_prime_UTR	Exon 12 of 12	NP_060705.2
	CNDP2	NM_001370248.1		c.*1044T>C		3_prime_UTR	Exon 12 of 12	NP_001357177.1
	CNDP2	NM_001370249.1		c.*1044T>C		3_prime_UTR	Exon 14 of 14	NP_001357178.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP2	ENST00000324262.9	TSL:1 MANE Select	c.*1044T>C		3_prime_UTR	Exon 12 of 12	ENSP00000325548.4
	CNDP2	ENST00000324301.12	TSL:1	c.*1044T>C		3_prime_UTR	Exon 9 of 9	ENSP00000325756.8
	CNDP2	ENST00000584581.5	TSL:2	n.4514T>C		non_coding_transcript_exon	Exon 6 of 6

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31330 AN: 152052 Hom.: 4090 Cov.: 33

Gnomad AFR AF: 0.0763

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.192

GnomAD4 exome AF: 0.250 AC: 7 AN: 28 Hom.: 0 Cov.: 0 AF XY: 0.227 AC XY: 5 AN XY: 22

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: 0.250 AC: 2 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.214 AC: 3 AN: 14

Other (OTH) AF: 0.333 AC: 2 AN: 6

GnomAD4 genome AF: 0.206 AC: 31341 AN: 152170 Hom.: 4089 Cov.: 33 AF XY: 0.204 AC XY: 15164 AN XY: 74390

African (AFR) AF: 0.0764 AC: 3171 AN: 41528

American (AMR) AF: 0.181 AC: 2760 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 712 AN: 3472

East Asian (EAS) AF: 0.0139 AC: 72 AN: 5176

South Asian (SAS) AF: 0.121 AC: 582 AN: 4826

European-Finnish (FIN) AF: 0.330 AC: 3488 AN: 10582

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19956 AN: 67988

Other (OTH) AF: 0.190 AC: 402 AN: 2112

Alfa AF: 0.253 Hom.: 9875

Bravo AF: 0.187

Asia WGS AF: 0.0720 AC: 259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.085
DANN	Benign	0.49
PhyloP100		-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: rs7577; hg19: chr18-72188347;