chr11-123115618-G-A

Variant names:

• chr11-123115618-G-A
• rs11605822
• NM_024769.5:c.29-17666C>T

Variant summary

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

The NM_024769.5(CLMP):​c.29-17666C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 151,864 control chromosomes in the GnomAD database, including 3,291 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 0.20 (3291 hom., cov: 31)
• Consequence: CLMP NM_024769.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 7 publications found

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]

CLMP Gene-Disease associations (from GenCC):

• congenital short bowel syndrome, autosomal recessive

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
• congenital short bowel syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000288061 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLMP	NM_024769.5	c.29-17666C>T		intron_variant	Intron 1 of 6	ENST00000448775.4	NP_079045.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLMP	ENST00000448775.4	c.29-17666C>T		intron_variant	Intron 1 of 6	1	NM_024769.5	ENSP00000405577.2
CLMP	ENST00000715744.1	c.29-17666C>T		intron_variant	Intron 1 of 6			ENSP00000520511.1
ENSG00000288061	ENST00000836643.1	n.226-20477G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31070 AN: 151744 Hom.: 3295 Cov.: 31

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.205 AC: 31074 AN: 151864 Hom.: 3291 Cov.: 31 AF XY: 0.205 AC XY: 15230 AN XY: 74230

African (AFR) AF: 0.187 AC: 7737 AN: 41418

American (AMR) AF: 0.277 AC: 4220 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 736 AN: 3468

East Asian (EAS) AF: 0.218 AC: 1121 AN: 5142

South Asian (SAS) AF: 0.171 AC: 824 AN: 4820

European-Finnish (FIN) AF: 0.179 AC: 1882 AN: 10524

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 13983 AN: 67952

Other (OTH) AF: 0.204 AC: 430 AN: 2106

Alfa AF: 0.211 Hom.: 6013

Bravo AF: 0.215

Asia WGS AF: 0.204 AC: 706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.36
PhyloP100		0.12
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: rs11605822; hg19: chr11-122986326;