18-74581582-T-C

Position:

• chr18-74581582-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.1309+1311T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 152,032 control chromosomes in the GnomAD database, including 34,741 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 0.67 (34741 hom., cov: 32)
• Consequence: CNDP1 NM_032649.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612

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]

LOC124904324 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNDP1	NM_032649.6	c.1309+1311T>C		intron_variant		ENST00000358821.8	NP_116038.4
LOC124904324	XR_007066415.1	n.1373A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNDP1	ENST00000358821.8	c.1309+1311T>C		intron_variant		1	NM_032649.6	ENSP00000351682.3
CNDP1	ENST00000582365.1	c.1180+1311T>C		intron_variant		5		ENSP00000462096.1
CNDP1	ENST00000582461.1	n.2190+1311T>C		intron_variant		5
CNDP1	ENST00000584004.5	n.833+1311T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102240 AN: 151914 Hom.: 34698 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.673 AC: 102335 AN: 152032 Hom.: 34741 Cov.: 32 AF XY: 0.679 AC XY: 50429 AN XY: 74318

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.761

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.704

Alfa AF: 0.662 Hom.: 6585

Bravo AF: 0.679

Asia WGS AF: 0.794 AC: 2764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.82
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: rs7244647; hg19: chr18-72248818;