chr18-74518403-G-T

Variant names:

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

Variant summary

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

The NM_018235.3(CNDP2):​c.1069-96G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0215 in 1,433,938 control chromosomes in the GnomAD database, including 667 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 0.039 (247 hom., cov: 33)
  • Exomes 𝑓: 0.019 (420 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0957 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.0394 AC: 6001 AN: 152154 Hom.: 247 Cov.: 33

Gnomad AFR AF: 0.0982

Gnomad AMI AF: 0.0769

Gnomad AMR AF: 0.0260

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0319

Gnomad FIN AF: 0.00650

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0160

Gnomad OTH AF: 0.0349

GnomAD4 exome AF: 0.0194 AC: 24825 AN: 1281666 Hom.: 420 Cov.: 18 AF XY: 0.0196 AC XY: 12533 AN XY: 639654

African (AFR) AF: 0.102 AC: 3050 AN: 29906

American (AMR) AF: 0.0145 AC: 605 AN: 41582

Ashkenazi Jewish (ASJ) AF: 0.00319 AC: 72 AN: 22564

East Asian (EAS) AF: 0.0218 AC: 841 AN: 38496

South Asian (SAS) AF: 0.0295 AC: 2246 AN: 76228

European-Finnish (FIN) AF: 0.00774 AC: 378 AN: 48816

Middle Eastern (MID) AF: 0.0148 AC: 77 AN: 5220

European-Non Finnish (NFE) AF: 0.0170 AC: 16375 AN: 964914

Other (OTH) AF: 0.0219 AC: 1181 AN: 53940

GnomAD4 genome AF: 0.0395 AC: 6014 AN: 152272 Hom.: 247 Cov.: 33 AF XY: 0.0390 AC XY: 2906 AN XY: 74458

African (AFR) AF: 0.0983 AC: 4081 AN: 41530

American (AMR) AF: 0.0260 AC: 398 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3472

East Asian (EAS) AF: 0.0137 AC: 71 AN: 5180

South Asian (SAS) AF: 0.0319 AC: 154 AN: 4822

European-Finnish (FIN) AF: 0.00650 AC: 69 AN: 10614

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

European-Non Finnish (NFE) AF: 0.0160 AC: 1089 AN: 68036

Other (OTH) AF: 0.0346 AC: 73 AN: 2112

Alfa AF: 0.0237 Hom.: 134

Bravo AF: 0.0434

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	0.54
PhyloP100		-2.2
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: rs17089362; hg19: chr18-72185638;