chr15-80946655-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001293298.2(CEMIP):​c.3858-310C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00906 in 386,650 control chromosomes in the GnomAD database, including 116 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.019 ( 101 hom., cov: 32)
Exomes 𝑓: 0.0027 ( 15 hom. )

Consequence

CEMIP
NM_001293298.2 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.910
Variant links:
Genes affected
CEMIP (HGNC:29213): (cell migration inducing hyaluronidase 1) Enables several functions, including clathrin heavy chain binding activity; hyaluronic acid binding activity; and hyalurononglucosaminidase activity. Involved in several processes, including hyaluronan catabolic process; positive regulation of protein phosphorylation; and positive regulation of transport. Located in clathrin-coated endocytic vesicle; endoplasmic reticulum; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
MESD (HGNC:13520): (mesoderm development LRP chaperone) Predicted to enable low-density lipoprotein particle receptor binding activity. Involved in ossification and protein folding. Located in endoplasmic reticulum. Implicated in osteogenesis imperfecta type 20. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 15-80946655-C-T is Benign according to our data. Variant chr15-80946655-C-T is described in ClinVar as [Benign]. Clinvar id is 1268091.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0635 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CEMIPNM_001293298.2 linkc.3858-310C>T intron_variant Intron 28 of 29 ENST00000394685.8 NP_001280227.1 Q8WUJ3-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CEMIPENST00000394685.8 linkc.3858-310C>T intron_variant Intron 28 of 29 1 NM_001293298.2 ENSP00000378177.3 Q8WUJ3-1

Frequencies

GnomAD3 genomes
AF:
0.0188
AC:
2855
AN:
152114
Hom.:
100
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0654
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00530
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000632
Gnomad OTH
AF:
0.0110
GnomAD4 exome
AF:
0.00270
AC:
632
AN:
234418
Hom.:
15
Cov.:
0
AF XY:
0.00240
AC XY:
301
AN XY:
125248
show subpopulations
Gnomad4 AFR exome
AF:
0.0620
Gnomad4 AMR exome
AF:
0.00508
Gnomad4 ASJ exome
AF:
0.000308
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000387
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000350
Gnomad4 OTH exome
AF:
0.00414
GnomAD4 genome
AF:
0.0189
AC:
2870
AN:
152232
Hom.:
101
Cov.:
32
AF XY:
0.0190
AC XY:
1412
AN XY:
74434
show subpopulations
Gnomad4 AFR
AF:
0.0656
Gnomad4 AMR
AF:
0.00529
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000618
Gnomad4 OTH
AF:
0.0109
Alfa
AF:
0.0104
Hom.:
6
Bravo
AF:
0.0212
Asia WGS
AF:
0.00375
AC:
13
AN:
3478

ClinVar

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

Submissions by phenotype

not provided Benign:1
Jun 19, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.95
DANN
Benign
0.65

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

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

Other links and lift over

dbSNP: rs115156548; hg19: chr15-81238996; API