rs11873377

Variant names:

• chr18-74495461-T-C
• rs11873377
• ENST00000969806.1:c.-38+1228T>C

Your query was ambiguous. Multiple possible variants found:

• chr18-74495461-T-C
• chr18-74495461-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000969806.1(CNDP2):​c.-38+1228T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,152 control chromosomes in the GnomAD database, including 1,558 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 0.11 (1558 hom., cov: 33)
• Consequence: CNDP2 ENST00000969806.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 2 publications found

Genes affected

CNDP2 (HGNC:24437): (carnosine dipeptidase 2) CNDP2, also known as tissue carnosinase and peptidase A (EC 3.4.13.18), is a nonspecific dipeptidase rather than a selective carnosinase (Teufel et al., 2003 [PubMed 12473676]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000969806.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP2	ENST00000969806.1		c.-38+1228T>C		intron	N/A	ENSP00000639865.1
	CNDP2	ENST00000969807.1		c.-93+1228T>C		intron	N/A	ENSP00000639866.1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16601 AN: 152034 Hom.: 1557 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0577

Gnomad ASJ AF: 0.0478

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0748

Gnomad FIN AF: 0.0552

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.0963

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

GnomAD4 genome AF: 0.109 AC: 16611 AN: 152152 Hom.: 1558 Cov.: 33 AF XY: 0.107 AC XY: 7989 AN XY: 74394

African (AFR) AF: 0.253 AC: 10505 AN: 41444

American (AMR) AF: 0.0575 AC: 879 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0478 AC: 166 AN: 3470

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5194

South Asian (SAS) AF: 0.0748 AC: 361 AN: 4824

European-Finnish (FIN) AF: 0.0552 AC: 585 AN: 10604

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0550 AC: 3739 AN: 68004

Other (OTH) AF: 0.0948 AC: 200 AN: 2110

Alfa AF: 0.0563 Hom.: 153

Bravo AF: 0.116

Asia WGS AF: 0.0430 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.38
PhyloP100		-1.0
PromoterAI		-0.011	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11873377; hg19: chr18-72162696;