chr5-10289925-G-A

Variant names:

• chr5-10289925-G-A
• rs13169284
• NM_138809.4:c.215+623C>T

Variant summary

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

The NM_138809.4(CMBL):​c.215+623C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 152,072 control chromosomes in the GnomAD database, including 19,124 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 0.44 (19124 hom., cov: 32)
• Consequence: CMBL NM_138809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384
• Publications: 2 publications found

Genes affected

CMBL (HGNC:25090): (carboxymethylenebutenolidase homolog) CMBL (EC 3.1.1.45) is a cysteine hydrolase of the dienelactone hydrolase family that is highly expressed in liver cytosol. CMBL preferentially cleaves cyclic esters, and it activates medoxomil-ester prodrugs in which the medoxomil moiety is linked to an oxygen atom (Ishizuka et al., 2010 [PubMed 20177059]).[supplied by OMIM, Apr 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138809.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CMBL	NM_138809.4	MANE Select	c.215+623C>T		intron	N/A	NP_620164.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CMBL	ENST00000296658.4	TSL:1 MANE Select	c.215+623C>T		intron	N/A	ENSP00000296658.3
	CMBL	ENST00000506821.1	TSL:2	n.469+623C>T		intron	N/A
	CMBL	ENST00000510532.5	TSL:3	n.283+623C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67191 AN: 151954 Hom.: 19129 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.0617

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.442 AC: 67175 AN: 152072 Hom.: 19124 Cov.: 32 AF XY: 0.438 AC XY: 32517 AN XY: 74322

African (AFR) AF: 0.121 AC: 5009 AN: 41516

American (AMR) AF: 0.396 AC: 6048 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2217 AN: 3470

East Asian (EAS) AF: 0.0618 AC: 320 AN: 5176

South Asian (SAS) AF: 0.337 AC: 1625 AN: 4824

European-Finnish (FIN) AF: 0.624 AC: 6575 AN: 10542

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43592 AN: 67942

Other (OTH) AF: 0.458 AC: 966 AN: 2110

Alfa AF: 0.554 Hom.: 24376

Bravo AF: 0.410

Asia WGS AF: 0.214 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.2
DANN	Benign	0.52
PhyloP100		0.38
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: rs13169284; hg19: chr5-10290037;