NM_032649.6:c.154-103A>T

Variant names:

• chr18-74559220-A-T
• rs12605490
• NM_032649.6:c.154-103A>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.154-103A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 1,172,228 control chromosomes in the GnomAD database, including 363,163 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 0.75 (43387 hom., cov: 31)
  • Exomes 𝑓: 0.79 (319776 hom.)
• Consequence: CNDP1 NM_032649.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.971
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 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.154-103A>T		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.154-103A>T		intron	N/A	ENSP00000351682.3
	CNDP1	ENST00000582365.1	TSL:5	c.25-103A>T		intron	N/A	ENSP00000462096.1
	CNDP1	ENST00000585136.1	TSL:3	n.319-103A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113433 AN: 151910 Hom.: 43357 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.767

GnomAD4 exome AF: 0.790 AC: 805679 AN: 1020200 Hom.: 319776 AF XY: 0.790 AC XY: 415610 AN XY: 526416

African (AFR) AF: 0.559 AC: 13614 AN: 24368

American (AMR) AF: 0.882 AC: 34010 AN: 38548

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 18487 AN: 22672

East Asian (EAS) AF: 0.940 AC: 35267 AN: 37538

South Asian (SAS) AF: 0.756 AC: 56830 AN: 75144

European-Finnish (FIN) AF: 0.848 AC: 40056 AN: 47226

Middle Eastern (MID) AF: 0.763 AC: 3007 AN: 3940

European-Non Finnish (NFE) AF: 0.784 AC: 568835 AN: 725286

Other (OTH) AF: 0.782 AC: 35573 AN: 45478

GnomAD4 genome AF: 0.747 AC: 113504 AN: 152028 Hom.: 43387 Cov.: 31 AF XY: 0.753 AC XY: 55939 AN XY: 74322

African (AFR) AF: 0.575 AC: 23812 AN: 41422

American (AMR) AF: 0.831 AC: 12710 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2869 AN: 3472

East Asian (EAS) AF: 0.932 AC: 4809 AN: 5160

South Asian (SAS) AF: 0.754 AC: 3628 AN: 4812

European-Finnish (FIN) AF: 0.859 AC: 9098 AN: 10588

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53934 AN: 67972

Other (OTH) AF: 0.769 AC: 1621 AN: 2108

Alfa AF: 0.763 Hom.: 5536

Bravo AF: 0.738

Asia WGS AF: 0.849 AC: 2951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.63
DANN	Benign	0.54
PhyloP100		-0.97
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: rs12605490; hg19: chr18-72226455; COSMIC: COSV62593480; COSMIC: COSV62593480;