rs733686

chr18-74555980-A-Gchr18-74555980-A-T

Variant summary

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

The NM_032649.6(CNDP1):c.25-358A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 151,608 control chromosomes in the GnomAD database, including 31,991 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 0.64 (31991 hom., cov: 32)
• Consequence: CNDP1 NM_032649.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.907

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNDP1	NM_032649.6	c.25-358A>G		intron_variant		ENST00000358821.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNDP1	ENST00000358821.8	c.25-358A>G		intron_variant		1	NM_032649.6	P1
CNDP1	ENST00000582365.1	c.25-3343A>G		intron_variant		5
CNDP1	ENST00000585136.1	n.190-358A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97140 AN: 151492 Hom.: 31982 Cov.: 32

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.641 AC: 97181 AN: 151608 Hom.: 31991 Cov.: 32 AF XY: 0.643 AC XY: 47652 AN XY: 74066

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.727

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.675

Alfa AF: 0.695 Hom.: 36346

Bravo AF: 0.636

Asia WGS AF: 0.671 AC: 2328 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.16
Dann	Benign	0.52

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: rs733686; hg19: chr18-72223215;