rs12574703

chr11-123152924-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024769.5(CLMP):c.28+41989C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.055 in 152,196 control chromosomes in the GnomAD database, including 371 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 0.055 (371 hom., cov: 32)
• Consequence: CLMP NM_024769.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.34

Genes affected

CLMP (HGNC:24039): (CXADR like membrane protein) This gene encodes a type I transmembrane protein that is localized to junctional complexes between endothelial and epithelial cells and may have a role in cell-cell adhesion. Expression of this gene in white adipose tissue is implicated in adipocyte maturation and development of obesity. This gene is also essential for normal intestinal development and mutations in the gene are associated with congenital short bowel syndrome. [provided by RefSeq, Aug 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLMP	NM_024769.5	c.28+41989C>T		intron_variant		ENST00000448775.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLMP	ENST00000448775.4	c.28+41989C>T		intron_variant		1	NM_024769.5	P1

Frequencies

GnomAD3 genomes AF: 0.0550 AC: 8368 AN: 152078 Hom.: 370 Cov.: 32

Gnomad AFR AF: 0.0353

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0712

Gnomad ASJ AF: 0.0761

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.0908

Gnomad FIN AF: 0.0212

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0509

Gnomad OTH AF: 0.0551

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

GnomAD4 genome AF: 0.0550 AC: 8371 AN: 152196 Hom.: 371 Cov.: 32 AF XY: 0.0576 AC XY: 4288 AN XY: 74412

Gnomad4 AFR AF: 0.0353

Gnomad4 AMR AF: 0.0710

Gnomad4 ASJ AF: 0.0761

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.0910

Gnomad4 FIN AF: 0.0212

Gnomad4 NFE AF: 0.0509

Gnomad4 OTH AF: 0.0565

Alfa AF: 0.0525 Hom.: 73

Bravo AF: 0.0582

Asia WGS AF: 0.152 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	13
Dann	Benign	0.37

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

Publications

LitVar

Other links and lift over

dbSNP: rs12574703; hg19: chr11-123023632;