rs8087768

Positions:

• chr18-74545837-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032649.6(CNDP1):​c.25-10501T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 152,002 control chromosomes in the GnomAD database, including 12,387 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 0.38 (12387 hom., cov: 32)
• Consequence: CNDP1 NM_032649.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNDP1	NM_032649.6	c.25-10501T>G		intron_variant		ENST00000358821.8	NP_116038.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNDP1	ENST00000358821.8	c.25-10501T>G		intron_variant		1	NM_032649.6	ENSP00000351682	P1
CNDP1	ENST00000582365.1	c.24+11146T>G		intron_variant		5		ENSP00000462096
CNDP1	ENST00000585136.1	n.190-10501T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57697 AN: 151884 Hom.: 12367 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.380 AC: 57765 AN: 152002 Hom.: 12387 Cov.: 32 AF XY: 0.382 AC XY: 28366 AN XY: 74278

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.397

Alfa AF: 0.314 Hom.: 4528

Bravo AF: 0.389

Asia WGS AF: 0.297 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.40

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: rs8087768; hg19: chr18-72213072;