rs11218950

chr11-123072200-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_024769.5(CLMP):c.*1274C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,176 control chromosomes in the GnomAD database, including 1,463 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 0.11 (1463 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: CLMP NM_024769.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLMP	NM_024769.5	c.*1274C>T		3_prime_UTR_variant	7/7	ENST00000448775.4
LOC124902775	XR_007062927.1	n.870+8669G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLMP	ENST00000448775.4	c.*1274C>T		3_prime_UTR_variant	7/7	1	NM_024769.5	P1
	ENST00000660892.2	n.226+8687G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16292 AN: 152058 Hom.: 1450 Cov.: 33

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0785

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0321

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0426

Gnomad OTH AF: 0.0809

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.107 AC: 16346 AN: 152176 Hom.: 1463 Cov.: 33 AF XY: 0.109 AC XY: 8077 AN XY: 74394

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.0785

Gnomad4 ASJ AF: 0.0303

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.0321

Gnomad4 NFE AF: 0.0425

Gnomad4 OTH AF: 0.0800

Alfa AF: 0.0657 Hom.: 403

Bravo AF: 0.114

Asia WGS AF: 0.164 AC: 569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
Cadd	Benign	7.7
Dann	Benign	0.83

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: rs11218950; hg19: chr11-122942908;