NM_032649.6:c.1309+743A>G

Variant names:

• chr18-74581014-A-G
• rs7242384
• NM_032649.6:c.1309+743A>G

Variant summary

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

The NM_032649.6(CNDP1):​c.1309+743A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 152,086 control chromosomes in the GnomAD database, including 19,333 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 0.47 (19333 hom., cov: 32)
• Consequence: CNDP1 NM_032649.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285
• Publications: 6 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNDP1	NM_032649.6	c.1309+743A>G		intron_variant	Intron 10 of 11	ENST00000358821.8	NP_116038.4
LOC124904324	XR_007066415.1	n.1941T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNDP1	ENST00000358821.8	c.1309+743A>G		intron_variant	Intron 10 of 11	1	NM_032649.6	ENSP00000351682.3
CNDP1	ENST00000582365.1	c.1180+743A>G		intron_variant	Intron 9 of 10	5		ENSP00000462096.1
CNDP1	ENST00000582461.1	n.2190+743A>G		intron_variant	Intron 2 of 2	5
CNDP1	ENST00000584004.5	n.833+743A>G		intron_variant	Intron 5 of 6	2

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71431 AN: 151968 Hom.: 19333 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.470 AC: 71433 AN: 152086 Hom.: 19333 Cov.: 32 AF XY: 0.475 AC XY: 35336 AN XY: 74338

African (AFR) AF: 0.178 AC: 7376 AN: 41518

American (AMR) AF: 0.596 AC: 9116 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1968 AN: 3468

East Asian (EAS) AF: 0.564 AC: 2911 AN: 5158

South Asian (SAS) AF: 0.571 AC: 2755 AN: 4824

European-Finnish (FIN) AF: 0.630 AC: 6656 AN: 10562

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 38978 AN: 67954

Other (OTH) AF: 0.499 AC: 1054 AN: 2112

Alfa AF: 0.529 Hom.: 35378

Bravo AF: 0.459

Asia WGS AF: 0.537 AC: 1868 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	2.9
DANN	Benign	0.58
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7242384; hg19: chr18-72248250;