chr18-74584850-A-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNDP1	NM_032649.6	c.*288A>C		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.*288A>C		3_prime_UTR_variant	Exon 12 of 12	1	NM_032649.6	ENSP00000351682.3
CNDP1	ENST00000582365.1	c.*288A>C		3_prime_UTR_variant	Exon 11 of 11	5		ENSP00000462096.1
CNDP1	ENST00000582461.1	n.3480A>C		non_coding_transcript_exon_variant	Exon 3 of 3	5
CNDP1	ENST00000584004.5	n.1336A>C		non_coding_transcript_exon_variant	Exon 7 of 7	2

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

Gnomad4 AFR exome AF: 0.964

Gnomad4 AMR exome AF: 0.997

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.997

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

Gnomad4 AFR AF: 0.964

Gnomad4 AMR AF: 0.995

Gnomad4 ASJ AF: 1.00

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 1.00

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 1.00

Gnomad4 OTH AF: 0.993

Alfa AF: 0.996 Hom.: 9575

Bravo AF: 0.988

Asia WGS AF: 0.999 AC: 3475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.8
DANN	Benign	0.32

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

Publications

LitVar

Other links and lift over

dbSNP: rs4891564; hg19: chr18-72252086;