chr18-74564245-T-C

Variant names:

• chr18-74564245-T-C
• rs11876996
• NM_032649.6:c.555+2110T>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.555+2110T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,946 control chromosomes in the GnomAD database, including 7,361 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 0.31 (7361 hom., cov: 32)
• Consequence: CNDP1 NM_032649.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 6 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 = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNDP1	NM_032649.6	c.555+2110T>C		intron_variant	Intron 5 of 11	ENST00000358821.8	NP_116038.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNDP1	ENST00000358821.8	c.555+2110T>C		intron_variant	Intron 5 of 11	1	NM_032649.6	ENSP00000351682.3
CNDP1	ENST00000582365.1	c.426+2110T>C		intron_variant	Intron 4 of 10	5		ENSP00000462096.1
CNDP1	ENST00000584316.5	n.*23+2110T>C		intron_variant	Intron 2 of 4	4		ENSP00000463807.1
CNDP1	ENST00000585136.1	n.557+2110T>C		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46416 AN: 151830 Hom.: 7357 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.297

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.306 AC: 46450 AN: 151946 Hom.: 7361 Cov.: 32 AF XY: 0.311 AC XY: 23130 AN XY: 74278

African (AFR) AF: 0.297 AC: 12308 AN: 41416

American (AMR) AF: 0.355 AC: 5429 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 928 AN: 3470

East Asian (EAS) AF: 0.533 AC: 2748 AN: 5154

South Asian (SAS) AF: 0.425 AC: 2046 AN: 4812

European-Finnish (FIN) AF: 0.314 AC: 3303 AN: 10528

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18786 AN: 67978

Other (OTH) AF: 0.299 AC: 631 AN: 2108

Alfa AF: 0.288 Hom.: 12140

Bravo AF: 0.307

Asia WGS AF: 0.465 AC: 1617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.028
DANN	Benign	0.42
PhyloP100		-1.7
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: rs11876996; hg19: chr18-72231480;