rs2887

Variant names:

• chr18-74584901-A-G
• rs2887
• NM_032649.6:c.*339A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 publications found

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]

ZNF407-AS1 (HGNC:44331): (ZNF407 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CNDP1	NM_032649.6	c.*339A>G		3_prime_UTR_variant	Exon 12 of 12	ENST00000358821.8	NP_116038.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNDP1	ENST00000358821.8	c.*339A>G		3_prime_UTR_variant	Exon 12 of 12	1	NM_032649.6	ENSP00000351682.3

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

African (AFR) AF: 0.465 AC: 1283 AN: 2762

American (AMR) AF: 0.703 AC: 2351 AN: 3346

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 1370 AN: 2180

East Asian (EAS) AF: 0.645 AC: 2893 AN: 4486

South Asian (SAS) AF: 0.725 AC: 1885 AN: 2600

European-Finnish (FIN) AF: 0.698 AC: 1577 AN: 2260

Middle Eastern (MID) AF: 0.693 AC: 158 AN: 228

European-Non Finnish (NFE) AF: 0.665 AC: 24034 AN: 36124

Other (OTH) AF: 0.662 AC: 2398 AN: 3622

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

African (AFR) AF: 0.475 AC: 19689 AN: 41452

American (AMR) AF: 0.693 AC: 10576 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2307 AN: 3472

East Asian (EAS) AF: 0.649 AC: 3343 AN: 5154

South Asian (SAS) AF: 0.727 AC: 3508 AN: 4824

European-Finnish (FIN) AF: 0.680 AC: 7194 AN: 10576

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45324 AN: 67962

Other (OTH) AF: 0.647 AC: 1365 AN: 2110

Alfa AF: 0.655 Hom.: 140293

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
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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