rs4891562

Variant names:

• chr18-74567102-A-C
• rs4891562
• NM_032649.6:c.556-131A>C

Your query was ambiguous. Multiple possible variants found:

• chr18-74567102-A-C
• chr18-74567102-A-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032649.6(CNDP1):​c.556-131A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 694,244 control chromosomes in the GnomAD database, including 132,748 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 0.56 (25158 hom., cov: 31)
  • Exomes 𝑓: 0.62 (107590 hom.)
• Consequence: CNDP1 NM_032649.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.02
• Publications: 3 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032649.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP1	NM_032649.6	MANE Select	c.556-131A>C		intron	N/A	NP_116038.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP1	ENST00000358821.8	TSL:1 MANE Select	c.556-131A>C		intron	N/A	ENSP00000351682.3
	CNDP1	ENST00000582365.1	TSL:5	c.427-131A>C		intron	N/A	ENSP00000462096.1
	CNDP1	ENST00000584316.5	TSL:4	n.*24-131A>C		intron	N/A	ENSP00000463807.1

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85030 AN: 151904 Hom.: 25152 Cov.: 31

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.590

GnomAD4 exome AF: 0.622 AC: 337219 AN: 542222 Hom.: 107590 AF XY: 0.619 AC XY: 179004 AN XY: 289094

African (AFR) AF: 0.357 AC: 5180 AN: 14498

American (AMR) AF: 0.576 AC: 16407 AN: 28468

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 10409 AN: 16300

East Asian (EAS) AF: 0.363 AC: 11591 AN: 31898

South Asian (SAS) AF: 0.539 AC: 28450 AN: 52812

European-Finnish (FIN) AF: 0.667 AC: 28040 AN: 42064

Middle Eastern (MID) AF: 0.623 AC: 1762 AN: 2828

European-Non Finnish (NFE) AF: 0.671 AC: 217444 AN: 324050

Other (OTH) AF: 0.612 AC: 17936 AN: 29304

GnomAD4 genome AF: 0.559 AC: 85051 AN: 152022 Hom.: 25158 Cov.: 31 AF XY: 0.557 AC XY: 41399 AN XY: 74330

African (AFR) AF: 0.362 AC: 15011 AN: 41434

American (AMR) AF: 0.569 AC: 8699 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2175 AN: 3468

East Asian (EAS) AF: 0.409 AC: 2113 AN: 5160

South Asian (SAS) AF: 0.529 AC: 2547 AN: 4812

European-Finnish (FIN) AF: 0.657 AC: 6946 AN: 10574

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.669 AC: 45476 AN: 67968

Other (OTH) AF: 0.589 AC: 1246 AN: 2114

Alfa AF: 0.486 Hom.: 1577

Bravo AF: 0.546

Asia WGS AF: 0.460 AC: 1598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.034
DANN	Benign	0.11
PhyloP100		-3.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4891562; hg19: chr18-72234337; COSMIC: COSV62594867; COSMIC: COSV62594867;