rs7952397

chr11-123186433-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+8480C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 151,968 control chromosomes in the GnomAD database, including 8,873 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 0.22 (8873 hom., cov: 32)
• Consequence: CLMP NM_024769.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLMP	NM_024769.5	c.28+8480C>T		intron_variant		ENST00000448775.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLMP	ENST00000448775.4	c.28+8480C>T		intron_variant		1	NM_024769.5	P1

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33752 AN: 151852 Hom.: 8829 Cov.: 32

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0654

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.223 AC: 33855 AN: 151968 Hom.: 8873 Cov.: 32 AF XY: 0.220 AC XY: 16377 AN XY: 74300

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.0767

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.0222

Gnomad4 FIN AF: 0.0654

Gnomad4 NFE AF: 0.0340

Gnomad4 OTH AF: 0.177

Alfa AF: 0.142 Hom.: 2084

Bravo AF: 0.258

Asia WGS AF: 0.136 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.39
Dann	Benign	0.55

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: rs7952397; hg19: chr11-123057141;