rs9967490

chr18-74561977-G-Achr18-74561977-G-T

Variant summary

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

The NM_032649.6(CNDP1):c.467-70G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 1,299,426 control chromosomes in the GnomAD database, including 60,057 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 0.35 (10704 hom., cov: 32)
  • Exomes 𝑓: 0.29 (49353 hom.)
• Consequence: CNDP1 NM_032649.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.44

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNDP1	NM_032649.6	c.467-70G>A		intron_variant		ENST00000358821.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNDP1	ENST00000358821.8	c.467-70G>A		intron_variant		1	NM_032649.6	P1
	ENST00000583702.1	n.104+20C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53192 AN: 151934 Hom.: 10685 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.337

GnomAD4 exome AF: 0.286 AC: 328391 AN: 1147374 Hom.: 49353 Cov.: 15 AF XY: 0.287 AC XY: 167780 AN XY: 584492

Gnomad4 AFR exome AF: 0.568

Gnomad4 AMR exome AF: 0.186

Gnomad4 ASJ exome AF: 0.336

Gnomad4 EAS exome AF: 0.119

Gnomad4 SAS exome AF: 0.323

Gnomad4 FIN exome AF: 0.212

Gnomad4 NFE exome AF: 0.288

Gnomad4 OTH exome AF: 0.306

GnomAD4 genome AF: 0.350 AC: 53250 AN: 152052 Hom.: 10704 Cov.: 32 AF XY: 0.344 AC XY: 25604 AN XY: 74326

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.332

Alfa AF: 0.294 Hom.: 9423

Bravo AF: 0.362

Asia WGS AF: 0.227 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.0020
Dann	Benign	0.38

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: rs9967490; hg19: chr18-72229212; COSMIC: COSV62595071;