rs12964208

Positions:

• chr18-74542955-G-A

Variant summary

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

The NM_032649.6(CNDP1):​c.24+8264G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 152,220 control chromosomes in the GnomAD database, including 22,135 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 0.53 (22135 hom., cov: 34)
• Consequence: CNDP1 NM_032649.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294

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 (AFR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNDP1	NM_032649.6	c.24+8264G>A		intron_variant		ENST00000358821.8	NP_116038.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNDP1	ENST00000358821.8	c.24+8264G>A		intron_variant		1	NM_032649.6	ENSP00000351682	P1
CNDP1	ENST00000582365.1	c.24+8264G>A		intron_variant		5		ENSP00000462096
CNDP1	ENST00000585136.1	n.189+8264G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80347 AN: 152102 Hom.: 22104 Cov.: 34

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.528 AC: 80435 AN: 152220 Hom.: 22135 Cov.: 34 AF XY: 0.526 AC XY: 39127 AN XY: 74400

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.531

Alfa AF: 0.494 Hom.: 38160

Bravo AF: 0.529

Asia WGS AF: 0.365 AC: 1271 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	0.90
DANN	Benign	0.28

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: rs12964208; hg19: chr18-72210190;