chr15-80880993-G-A

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_001293298.2(CEMIP):​c.474G>A​(p.Lys158=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00492 in 1,614,210 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0033 ( 4 hom., cov: 33)
Exomes 𝑓: 0.0051 ( 27 hom. )

Consequence

CEMIP
NM_001293298.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.59
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
Variant 15-80880993-G-A is Benign according to our data. Variant chr15-80880993-G-A is described in ClinVar as [Benign]. Clinvar id is 770434.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=2.59 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CEMIPNM_001293298.2 linkuse as main transcriptc.474G>A p.Lys158= synonymous_variant 6/30 ENST00000394685.8 NP_001280227.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CEMIPENST00000394685.8 linkuse as main transcriptc.474G>A p.Lys158= synonymous_variant 6/301 NM_001293298.2 ENSP00000378177 P1Q8WUJ3-1
CEMIPENST00000220244.7 linkuse as main transcriptc.474G>A p.Lys158= synonymous_variant 5/291 ENSP00000220244 P1Q8WUJ3-1
CEMIPENST00000356249.9 linkuse as main transcriptc.474G>A p.Lys158= synonymous_variant 6/301 ENSP00000348583 P1Q8WUJ3-1

Frequencies

GnomAD3 genomes
AF:
0.00332
AC:
506
AN:
152216
Hom.:
4
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00109
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.00111
Gnomad ASJ
AF:
0.000865
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00490
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00558
Gnomad OTH
AF:
0.00335
GnomAD3 exomes
AF:
0.00385
AC:
968
AN:
251424
Hom.:
5
AF XY:
0.00372
AC XY:
506
AN XY:
135878
show subpopulations
Gnomad AFR exome
AF:
0.00129
Gnomad AMR exome
AF:
0.000954
Gnomad ASJ exome
AF:
0.000496
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000980
Gnomad FIN exome
AF:
0.00855
Gnomad NFE exome
AF:
0.00617
Gnomad OTH exome
AF:
0.00326
GnomAD4 exome
AF:
0.00508
AC:
7430
AN:
1461876
Hom.:
27
Cov.:
32
AF XY:
0.00484
AC XY:
3523
AN XY:
727242
show subpopulations
Gnomad4 AFR exome
AF:
0.000657
Gnomad4 AMR exome
AF:
0.000917
Gnomad4 ASJ exome
AF:
0.000842
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000348
Gnomad4 FIN exome
AF:
0.00833
Gnomad4 NFE exome
AF:
0.00603
Gnomad4 OTH exome
AF:
0.00321
GnomAD4 genome
AF:
0.00332
AC:
506
AN:
152334
Hom.:
4
Cov.:
33
AF XY:
0.00298
AC XY:
222
AN XY:
74488
show subpopulations
Gnomad4 AFR
AF:
0.00108
Gnomad4 AMR
AF:
0.00111
Gnomad4 ASJ
AF:
0.000865
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00490
Gnomad4 NFE
AF:
0.00559
Gnomad4 OTH
AF:
0.00331
Alfa
AF:
0.00363
Hom.:
0
Bravo
AF:
0.00298
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.00458
EpiControl
AF:
0.00551

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.51
CADD
Benign
7.0
DANN
Benign
0.50

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: rs72740115; hg19: chr15-81173334; COSMIC: COSV54989707; API