rs11605822

chr11-123115618-G-Achr11-123115618-G-C

Variant summary

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

The NM_024769.5(CLMP):c.29-17666C>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

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=-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/exons	MANE	UniProt
CLMP	NM_024769.5	c.29-17666C>T		intron_variant		ENST00000448775.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLMP	ENST00000448775.4	c.29-17666C>T		intron_variant		1	NM_024769.5	P1

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

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.204

Alfa AF: 0.211 Hom.: 4771

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

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: rs11605822; hg19: chr11-122986326;