dbSNP rs35541581: CEMIP:p.Leu83Leu (chr15-80879723-G-A) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001293298.2(CEMIP):c.249G>A(p.Leu83Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0136 in 1,614,116 control chromosomes in the GnomAD database, including 1,966 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.064 ( 1042 hom., cov: 33)

Exomes 𝑓: 0.0083 ( 924 hom. )

Consequence

CEMIP
NM_001293298.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -2.25

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]

CEMIP links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 15-80879723-G-A is Benign according to our data. Variant chr15-80879723-G-A is described in ClinVar as [Benign]. Clinvar id is 585660.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.26 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEMIP	NM_001293298.2 link	c.249G>A	p.Leu83Leu	synonymous_variant	Exon 5 of 30	ENST00000394685.8	NP_001280227.1	Q8WUJ3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
CEMIP	ENST00000394685.8 link	c.249G>A	p.Leu83Leu	synonymous_variant	Exon 5 of 30	1	NM_001293298.2	ENSP00000378177.3	Q8WUJ3-1
CEMIP	ENST00000220244.7 link	c.249G>A	p.Leu83Leu	synonymous_variant	Exon 4 of 29	1		ENSP00000220244.3	Q8WUJ3-1
CEMIP	ENST00000356249.9 link	c.249G>A	p.Leu83Leu	synonymous_variant	Exon 5 of 30	1		ENSP00000348583.5	Q8WUJ3-1

Frequencies

GnomAD3 genomes

AF:

0.0638

AC:

9702

AN:

152136

Hom.:

1033

Cov.:

show subpopulations

Gnomad AFR

AF:

0.216

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0287

Gnomad ASJ

AF:

0.00749

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.00103

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.00272

Gnomad OTH

AF:

0.0469

GnomAD3 exomes

AF:

0.0185

AC:

4644

AN:

251230

Hom.:

440

AF XY:

0.0138

AC XY:

1878

AN XY:

135780

show subpopulations

Gnomad AFR exome

AF:

0.225

Gnomad AMR exome

AF:

0.0150

Gnomad ASJ exome

AF:

0.00774

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.000425

Gnomad FIN exome

AF:

0.0000924

Gnomad NFE exome

AF:

0.00263

Gnomad OTH exome

AF:

0.0134

GnomAD4 exome

AF:

0.00831

AC:

12155

AN:

1461862

Hom.:

924

Cov.:

AF XY:

0.00734

AC XY:

5336

AN XY:

727238

show subpopulations

Gnomad4 AFR exome

AF:

0.225

Gnomad4 AMR exome

AF:

0.0168

Gnomad4 ASJ exome

AF:

0.00754

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.000533

Gnomad4 FIN exome

AF:

0.0000936

Gnomad4 NFE exome

AF:

0.00219

Gnomad4 OTH exome

AF:

0.0177

GnomAD4 genome

AF:

0.0640

AC:

9742

AN:

152254

Hom.:

1042

Cov.:

AF XY:

0.0623

AC XY:

4641

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.216

Gnomad4 AMR

AF:

0.0285

Gnomad4 ASJ

AF:

0.00749

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.000828

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00272

Gnomad4 OTH

AF:

0.0483

Alfa

AF:

0.0305

Hom.:

220

Bravo

AF:

0.0727

Asia WGS

AF:

0.0150

AC:

AN:

3478

EpiCase

AF:

0.00431

EpiControl

AF:

0.00284

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

May 05, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

May 23, 2018

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

CEMIP-related disorder

Benign:1

Nov 25, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.038

DANN

Benign

0.52

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over