18-74574100-T-G

Variant names:

• chr18-74574100-T-G
• rs7506957
• NM_032649.6:c.842-2769T>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.842-2769T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 152,116 control chromosomes in the GnomAD database, including 31,866 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 0.64 (31866 hom., cov: 33)
• Consequence: CNDP1 NM_032649.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 2 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNDP1	NM_032649.6	c.842-2769T>G		intron_variant	Intron 7 of 11	ENST00000358821.8	NP_116038.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNDP1	ENST00000358821.8	c.842-2769T>G		intron_variant	Intron 7 of 11	1	NM_032649.6	ENSP00000351682.3
CNDP1	ENST00000582365.1	c.713-2769T>G		intron_variant	Intron 6 of 10	5		ENSP00000462096.1
CNDP1	ENST00000584004.5	n.366-2769T>G		intron_variant	Intron 2 of 6	2
CNDP1	ENST00000584316.5	n.*310-2509T>G		intron_variant	Intron 4 of 4	4		ENSP00000463807.1

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97216 AN: 151998 Hom.: 31831 Cov.: 33

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.640 AC: 97308 AN: 152116 Hom.: 31866 Cov.: 33 AF XY: 0.640 AC XY: 47556 AN XY: 74354

African (AFR) AF: 0.767 AC: 31831 AN: 41496

American (AMR) AF: 0.708 AC: 10822 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1759 AN: 3470

East Asian (EAS) AF: 0.696 AC: 3594 AN: 5162

South Asian (SAS) AF: 0.684 AC: 3298 AN: 4824

European-Finnish (FIN) AF: 0.507 AC: 5365 AN: 10574

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38568 AN: 67976

Other (OTH) AF: 0.638 AC: 1350 AN: 2116

Alfa AF: 0.604 Hom.: 3686

Bravo AF: 0.661

Asia WGS AF: 0.740 AC: 2574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.64
PhyloP100		-0.016
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: rs7506957; hg19: chr18-72241335;