Genetic Variant CNDP2:c.*309C>T (chr18-74520377-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018235.3(CNDP2):c.*309C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.952 in 331,202 control chromosomes in the GnomAD database, including 151,755 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 ( 64618 hom., cov: 32)

Exomes 𝑓: 0.99 ( 87137 hom. )

Consequence

CNDP2
NM_018235.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.258

Variant links:

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]

CNDP2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNDP2	NM_018235.3 link	c.*309C>T		3_prime_UTR_variant	Exon 12 of 12	ENST00000324262.9	NP_060705.2	Q96KP4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNDP2	ENST00000324262.9 link	c.*309C>T		3_prime_UTR_variant	Exon 12 of 12	1	NM_018235.3	ENSP00000325548.4		Q96KP4-1

Frequencies

GnomAD3 genomes

AF:

0.913

AC:

138831

AN:

152122

Hom.:

64598

Cov.:

show subpopulations

Gnomad AFR

AF:

0.711

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.961

Gnomad ASJ

AF:

1.00

Gnomad EAS

AF:

0.900

Gnomad SAS

AF:

0.999

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.978

Gnomad NFE

AF:

0.999

Gnomad OTH

AF:

0.939

GnomAD4 exome

AF:

0.986

AC:

176410

AN:

178962

Hom.:

87137

Cov.:

AF XY:

0.988

AC XY:

93927

AN XY:

95108

show subpopulations

Gnomad4 AFR exome

AF:

0.737

Gnomad4 AMR exome

AF:

0.977

Gnomad4 ASJ exome

AF:

1.00

Gnomad4 EAS exome

AF:

0.914

Gnomad4 SAS exome

AF:

0.999

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.999

Gnomad4 OTH exome

AF:

0.975

GnomAD4 genome

AF:

0.912

AC:

138891

AN:

152240

Hom.:

64618

Cov.:

AF XY:

0.915

AC XY:

68089

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.711

Gnomad4 AMR

AF:

0.961

Gnomad4 ASJ

AF:

1.00

Gnomad4 EAS

AF:

0.900

Gnomad4 SAS

AF:

0.999

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

0.999

Gnomad4 OTH

AF:

0.938

Alfa

AF:

0.985

Hom.:

67925

Bravo

AF:

0.900

Asia WGS

AF:

0.945

AC:

3285

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

0.89

DANN

Benign

0.48

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over