Variant 18-74567400-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_032649.6(CNDP1):c.723C>T(p.Tyr241=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 1,613,224 control chromosomes in the GnomAD database, including 332,887 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 0.55 ( 24682 hom., cov: 32)

Exomes 𝑓: 0.64 ( 308205 hom. )

Consequence

CNDP1
NM_032649.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.781

Variant links:

Genes affected

CNDP1 (HGNC:20675): (carnosine dipeptidase 1) This gene encodes a member of the M20 metalloprotease family. The encoded protein is specifically expressed in the brain, is a homodimeric dipeptidase which was identified as human carnosinase. This gene contains trinucleotide (CTG) repeat length polymorphism in the coding region. [provided by RefSeq, Jul 2008]

CNDP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP7

Synonymous conserved (PhyloP=-0.781 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNDP1	NM_032649.6 linkuse as main transcript	c.723C>T	p.Tyr241=	synonymous_variant	6/12	ENST00000358821.8	NP_116038.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
CNDP1	ENST00000358821.8 linkuse as main transcript	c.723C>T	p.Tyr241=	synonymous_variant	6/12	1	NM_032649.6	ENSP00000351682	P1
CNDP1	ENST00000582365.1 linkuse as main transcript	c.594C>T	p.Tyr198=	synonymous_variant	5/11	5		ENSP00000462096
CNDP1	ENST00000584004.5 linkuse as main transcript	n.247C>T		non_coding_transcript_exon_variant	1/7	2
CNDP1	ENST00000584316.5 linkuse as main transcript	c.*191C>T		3_prime_UTR_variant, NMD_transcript_variant	3/5	4		ENSP00000463807

Frequencies

GnomAD3 genomes

AF:

0.553

AC:

83999

AN:

151952

Hom.:

24678

Cov.:

show subpopulations

Gnomad AFR

AF:

0.349

Gnomad AMI

AF:

0.737

Gnomad AMR

AF:

0.547

Gnomad ASJ

AF:

0.626

Gnomad EAS

AF:

0.409

Gnomad SAS

AF:

0.520

Gnomad FIN

AF:

0.657

Gnomad MID

AF:

0.570

Gnomad NFE

AF:

0.668

Gnomad OTH

AF:

0.579

GnomAD3 exomes

AF:

0.591

AC:

148375

AN:

251260

Hom.:

45340

AF XY:

0.595

AC XY:

80763

AN XY:

135798

show subpopulations

Gnomad AFR exome

AF:

0.342

Gnomad AMR exome

AF:

0.550

Gnomad ASJ exome

AF:

0.637

Gnomad EAS exome

AF:

0.425

Gnomad SAS exome

AF:

0.525

Gnomad FIN exome

AF:

0.663

Gnomad NFE exome

AF:

0.663

Gnomad OTH exome

AF:

0.621

GnomAD4 exome

AF:

0.644

AC:

940767

AN:

1461154

Hom.:

308205

Cov.:

AF XY:

0.641

AC XY:

465955

AN XY:

726924

show subpopulations

Gnomad4 AFR exome

AF:

0.334

Gnomad4 AMR exome

AF:

0.551

Gnomad4 ASJ exome

AF:

0.637

Gnomad4 EAS exome

AF:

0.369

Gnomad4 SAS exome

AF:

0.532

Gnomad4 FIN exome

AF:

0.666

Gnomad4 NFE exome

AF:

0.676

Gnomad4 OTH exome

AF:

0.615

GnomAD4 genome

AF:

0.552

AC:

84014

AN:

152070

Hom.:

24682

Cov.:

AF XY:

0.550

AC XY:

40872

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.349

Gnomad4 AMR

AF:

0.547

Gnomad4 ASJ

AF:

0.626

Gnomad4 EAS

AF:

0.408

Gnomad4 SAS

AF:

0.520

Gnomad4 FIN

AF:

0.657

Gnomad4 NFE

AF:

0.668

Gnomad4 OTH

AF:

0.579

Alfa

AF:

0.642

Hom.:

74309

Bravo

AF:

0.537

Asia WGS

AF:

0.455

AC:

1580

AN:

3478

EpiCase

AF:

0.668

EpiControl

AF:

0.668

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

0.015

DANN

Benign

0.26

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