NM_032649.6:c.*288A>C

Variant names:

• chr18-74584850-A-C
• rs4891564
• NM_032649.6:c.*288A>C

Variant summary

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

The NM_032649.6(CNDP1):​c.*288A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.994 in 352,898 control chromosomes in the GnomAD database, including 174,538 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 0.99 (74625 hom., cov: 33)
  • Exomes 𝑓: 1.0 (99913 hom.)
• Consequence: CNDP1 NM_032649.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.659
• 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]

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP1	NM_032649.6	MANE Select	c.*288A>C		3_prime_UTR	Exon 12 of 12	NP_116038.4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP1	ENST00000358821.8	TSL:1 MANE Select	c.*288A>C		3_prime_UTR	Exon 12 of 12	ENSP00000351682.3	Q96KN2
	CNDP1	ENST00000864762.1		c.*288A>C		3_prime_UTR	Exon 12 of 12	ENSP00000534821.1
	CNDP1	ENST00000954332.1		c.*288A>C		3_prime_UTR	Exon 12 of 12	ENSP00000624391.1

Frequencies

GnomAD3 genomes AF: 0.990 AC: 150654 AN: 152236 Hom.: 74568 Cov.: 33

Gnomad AFR AF: 0.964

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.995

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.993

GnomAD4 exome AF: 0.998 AC: 200179 AN: 200544 Hom.: 99913 Cov.: 2 AF XY: 0.998 AC XY: 102890 AN XY: 103046

African (AFR) AF: 0.964 AC: 7559 AN: 7842

American (AMR) AF: 0.997 AC: 8773 AN: 8796

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 7168 AN: 7168

East Asian (EAS) AF: 1.00 AC: 17172 AN: 17172

South Asian (SAS) AF: 1.00 AC: 10193 AN: 10194

European-Finnish (FIN) AF: 1.00 AC: 11598 AN: 11598

Middle Eastern (MID) AF: 0.999 AC: 925 AN: 926

European-Non Finnish (NFE) AF: 1.00 AC: 124227 AN: 124242

Other (OTH) AF: 0.997 AC: 12564 AN: 12606

GnomAD4 genome AF: 0.990 AC: 150770 AN: 152354 Hom.: 74625 Cov.: 33 AF XY: 0.990 AC XY: 73751 AN XY: 74496

African (AFR) AF: 0.964 AC: 40107 AN: 41584

American (AMR) AF: 0.995 AC: 15229 AN: 15308

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5180 AN: 5180

South Asian (SAS) AF: 1.00 AC: 4824 AN: 4824

European-Finnish (FIN) AF: 1.00 AC: 10622 AN: 10622

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 68035 AN: 68048

Other (OTH) AF: 0.993 AC: 2097 AN: 2112

Alfa AF: 0.995 Hom.: 20382

Bravo AF: 0.988

Asia WGS AF: 0.999 AC: 3475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.8
DANN	Benign	0.32
PhyloP100		0.66
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: rs4891564; hg19: chr18-72252086;