11-123115764-T-C

Position:

• chr11-123115764-T-C

Variant summary

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

The NM_024769.5(CLMP):​c.29-17812A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,088 control chromosomes in the GnomAD database, including 4,148 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 0.23 (4148 hom., cov: 31)
• Consequence: CLMP NM_024769.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.389

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLMP	NM_024769.5	c.29-17812A>G		intron_variant		ENST00000448775.4	NP_079045.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLMP	ENST00000448775.4	c.29-17812A>G		intron_variant		1	NM_024769.5	ENSP00000405577.2

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34768 AN: 151968 Hom.: 4149 Cov.: 31

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.229 AC: 34783 AN: 152088 Hom.: 4148 Cov.: 31 AF XY: 0.229 AC XY: 16989 AN XY: 74340

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.218

Alfa AF: 0.185 Hom.: 1318

Bravo AF: 0.242

Asia WGS AF: 0.216 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.5
DANN	Benign	0.50

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: rs11607994; hg19: chr11-122986472;