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GeneBe

11-123073585-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_024769.5(CLMP):c.1011G>A(p.Gly337=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0083 in 1,614,246 control chromosomes in the GnomAD database, including 88 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0058 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0086 ( 85 hom. )

Consequence

CLMP
NM_024769.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.796
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-123073585-C-T is Benign according to our data. Variant chr11-123073585-C-T is described in ClinVar as [Benign]. Clinvar id is 787547.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.796 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00578 (880/152354) while in subpopulation SAS AF= 0.0217 (105/4830). AF 95% confidence interval is 0.0184. There are 3 homozygotes in gnomad4. There are 446 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CLMPNM_024769.5 linkuse as main transcriptc.1011G>A p.Gly337= synonymous_variant 7/7 ENST00000448775.4
LOC124902775XR_007062927.1 linkuse as main transcriptn.871-9429C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CLMPENST00000448775.4 linkuse as main transcriptc.1011G>A p.Gly337= synonymous_variant 7/71 NM_024769.5 P1
ENST00000660892.2 linkuse as main transcriptn.226+10072C>T intron_variant, non_coding_transcript_variant
CLMPENST00000530371.5 linkuse as main transcriptn.485G>A non_coding_transcript_exon_variant 4/44

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00577
AC:
879
AN:
152234
Hom.:
3
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00176
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00458
Gnomad ASJ
AF:
0.0141
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0215
Gnomad FIN
AF:
0.00339
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00786
Gnomad OTH
AF:
0.00573
GnomAD3 exomes
AF:
0.00703
AC:
1767
AN:
251486
Hom.:
19
AF XY:
0.00828
AC XY:
1126
AN XY:
135918
show subpopulations
Gnomad AFR exome
AF:
0.00117
Gnomad AMR exome
AF:
0.00234
Gnomad ASJ exome
AF:
0.0122
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.0202
Gnomad FIN exome
AF:
0.00273
Gnomad NFE exome
AF:
0.00719
Gnomad OTH exome
AF:
0.00798
GnomAD4 exome
AF:
0.00856
AC:
12511
AN:
1461892
Hom.:
85
Cov.:
31
AF XY:
0.00884
AC XY:
6431
AN XY:
727248
show subpopulations
Gnomad4 AFR exome
AF:
0.00125
Gnomad4 AMR exome
AF:
0.00230
Gnomad4 ASJ exome
AF:
0.0145
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0200
Gnomad4 FIN exome
AF:
0.00249
Gnomad4 NFE exome
AF:
0.00863
Gnomad4 OTH exome
AF:
0.00755
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00578
AC:
880
AN:
152354
Hom.:
3
Cov.:
32
AF XY:
0.00599
AC XY:
446
AN XY:
74492
show subpopulations
Gnomad4 AFR
AF:
0.00176
Gnomad4 AMR
AF:
0.00458
Gnomad4 ASJ
AF:
0.0141
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0217
Gnomad4 FIN
AF:
0.00339
Gnomad4 NFE
AF:
0.00786
Gnomad4 OTH
AF:
0.00567
Alfa
AF:
0.00752
Hom.:
4
Bravo
AF:
0.00484
Asia WGS
AF:
0.00751
AC:
26
AN:
3478
EpiCase
AF:
0.00911
EpiControl
AF:
0.00818

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
Cadd
Benign
10
Dann
Benign
0.52

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.18
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs142456942; hg19: chr11-122944293; API