rs2887

Positions:

• chr18-74584901-A-G
• chr18-74584901-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032649.6(CNDP1):​c.*339A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 209,634 control chromosomes in the GnomAD database, including 42,375 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 0.62 (29776 hom., cov: 32)
  • Exomes 𝑓: 0.66 (12599 hom.)
• Consequence: CNDP1 NM_032649.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNDP1	NM_032649.6	c.*339A>G		3_prime_UTR_variant	12/12	ENST00000358821.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNDP1	ENST00000358821.8	c.*339A>G		3_prime_UTR_variant	12/12	1	NM_032649.6	P1
CNDP1	ENST00000582365.1	c.*339A>G		3_prime_UTR_variant	11/11	5
CNDP1	ENST00000582461.1	n.3531A>G		non_coding_transcript_exon_variant	3/3	5
CNDP1	ENST00000584004.5	n.1387A>G		non_coding_transcript_exon_variant	7/7	2

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94033 AN: 151906 Hom.: 29756 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.650

GnomAD4 exome AF: 0.659 AC: 37949 AN: 57608 Hom.: 12599 Cov.: 0 AF XY: 0.661 AC XY: 19680 AN XY: 29768

Gnomad4 AFR exome AF: 0.465

Gnomad4 AMR exome AF: 0.703

Gnomad4 ASJ exome AF: 0.628

Gnomad4 EAS exome AF: 0.645

Gnomad4 SAS exome AF: 0.725

Gnomad4 FIN exome AF: 0.698

Gnomad4 NFE exome AF: 0.665

Gnomad4 OTH exome AF: 0.662

GnomAD4 genome AF: 0.619 AC: 94100 AN: 152026 Hom.: 29776 Cov.: 32 AF XY: 0.622 AC XY: 46227 AN XY: 74308

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.647

Alfa AF: 0.664 Hom.: 68565

Bravo AF: 0.617

Asia WGS AF: 0.676 AC: 2352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		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

Other links and lift over

dbSNP: rs2887; hg19: chr18-72252137; COSMIC: COSV105269023;