rs11876996

chr18-74564245-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.92).
• 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/exons	MANE	UniProt
CNDP1	NM_032649.6	c.555+2110T>C		intron_variant		ENST00000358821.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNDP1	ENST00000358821.8	c.555+2110T>C		intron_variant		1	NM_032649.6	P1
CNDP1	ENST00000582365.1	c.426+2110T>C		intron_variant		5
CNDP1	ENST00000584316.5	c.*23+2110T>C		intron_variant, NMD_transcript_variant		4
CNDP1	ENST00000585136.1	n.557+2110T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.299

Alfa AF: 0.283 Hom.: 8578

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

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: rs11876996; hg19: chr18-72231480;