Variant rs2241511 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_018235.3(CNDP2):c.743-71G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 1,452,442 control chromosomes in the GnomAD database, including 148,222 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 0.43 ( 14210 hom., cov: 34)

Exomes 𝑓: 0.45 ( 134012 hom. )

Consequence

CNDP2
NM_018235.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.846

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNDP2	NM_018235.3 linkuse as main transcript	c.743-71G>A		intron_variant		ENST00000324262.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNDP2	ENST00000324262.9 linkuse as main transcript	c.743-71G>A		intron_variant		1	NM_018235.3	P1	Q96KP4-1

Frequencies

GnomAD3 genomes

AF:

0.426

AC:

64813

AN:

152014

Hom.:

14200

Cov.:

show subpopulations

Gnomad AFR

AF:

0.333

Gnomad AMI

AF:

0.507

Gnomad AMR

AF:

0.449

Gnomad ASJ

AF:

0.542

Gnomad EAS

AF:

0.665

Gnomad SAS

AF:

0.466

Gnomad FIN

AF:

0.438

Gnomad MID

AF:

0.491

Gnomad NFE

AF:

0.448

Gnomad OTH

AF:

0.427

GnomAD4 exome

AF:

0.451

AC:

587035

AN:

1300310

Hom.:

134012

AF XY:

0.451

AC XY:

287034

AN XY:

636190

show subpopulations

Gnomad4 AFR exome

AF:

0.331

Gnomad4 AMR exome

AF:

0.470

Gnomad4 ASJ exome

AF:

0.551

Gnomad4 EAS exome

AF:

0.664

Gnomad4 SAS exome

AF:

0.457

Gnomad4 FIN exome

AF:

0.454

Gnomad4 NFE exome

AF:

0.444

Gnomad4 OTH exome

AF:

0.472

GnomAD4 genome

AF:

0.426

AC:

64852

AN:

152132

Hom.:

14210

Cov.:

AF XY:

0.429

AC XY:

31870

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.333

Gnomad4 AMR

AF:

0.448

Gnomad4 ASJ

AF:

0.542

Gnomad4 EAS

AF:

0.665

Gnomad4 SAS

AF:

0.466

Gnomad4 FIN

AF:

0.438

Gnomad4 NFE

AF:

0.448

Gnomad4 OTH

AF:

0.432

Alfa

AF:

0.430

Hom.:

2122

Bravo

AF:

0.424

Asia WGS

AF:

0.537

AC:

1864

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.66

DANN

Benign

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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