ENST00000969806.1:c.-38+1692C>T

Variant names:

• chr18-74495925-C-T
• rs7237740
• ENST00000969806.1:c.-38+1692C>T

Variant summary

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

The ENST00000969806.1(CNDP2):​c.-38+1692C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,362 control chromosomes in the GnomAD database, including 14,149 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 0.42 (14113 hom., cov: 32)
  • Exomes 𝑓: 0.50 (36 hom.)
• Consequence: CNDP2 ENST00000969806.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 5 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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 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+1692C>T		intron	N/A	ENSP00000639865.1
	CNDP2	ENST00000969807.1		c.-93+1692C>T		intron	N/A	ENSP00000639866.1
	CNDP2	ENST00000581272.5	TSL:4	c.-38+2C>T		splice_donor intron	N/A	ENSP00000464151.1	J3QRD0

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64594 AN: 151966 Hom.: 14103 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.423

GnomAD4 exome AF: 0.496 AC: 138 AN: 278 Hom.: 36 Cov.: 0 AF XY: 0.500 AC XY: 107 AN XY: 214

African (AFR) AF: 0.500 AC: 4 AN: 8

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.833 AC: 5 AN: 6

South Asian (SAS) AF: 0.500 AC: 2 AN: 4

European-Finnish (FIN) AF: 0.500 AC: 4 AN: 8

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.487 AC: 113 AN: 232

Other (OTH) AF: 0.500 AC: 7 AN: 14

GnomAD4 genome AF: 0.425 AC: 64629 AN: 152084 Hom.: 14113 Cov.: 32 AF XY: 0.427 AC XY: 31729 AN XY: 74316

African (AFR) AF: 0.333 AC: 13822 AN: 41508

American (AMR) AF: 0.453 AC: 6928 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1888 AN: 3470

East Asian (EAS) AF: 0.684 AC: 3521 AN: 5146

South Asian (SAS) AF: 0.452 AC: 2178 AN: 4818

European-Finnish (FIN) AF: 0.415 AC: 4385 AN: 10576

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30395 AN: 67968

Other (OTH) AF: 0.427 AC: 901 AN: 2112

Alfa AF: 0.431 Hom.: 1884

Bravo AF: 0.426

Asia WGS AF: 0.520 AC: 1805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.1
DANN	Benign	0.81
PhyloP100		-1.6
PromoterAI		-0.11	Neutral

Splicing

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

Other links and lift over

dbSNP: rs7237740; hg19: chr18-72163160;