Variant chr15-80929151-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_001293298.2(CEMIP):c.2589C>T(p.Ser863=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0217 in 1,614,100 control chromosomes in the GnomAD database, including 418 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.024 ( 52 hom., cov: 32)

Exomes 𝑓: 0.022 ( 366 hom. )

Consequence

CEMIP
NM_001293298.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -4.91

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=-0.84).

BP6

Variant 15-80929151-C-T is Benign according to our data. Variant chr15-80929151-C-T is described in ClinVar as [Benign]. Clinvar id is 585661.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-4.91 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.024 (3647/152222) while in subpopulation AFR AF= 0.0281 (1169/41542). AF 95% confidence interval is 0.0268. There are 52 homozygotes in gnomad4. There are 1651 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 52 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEMIP	NM_001293298.2 linkuse as main transcript	c.2589C>T	p.Ser863=	synonymous_variant	21/30	ENST00000394685.8	NP_001280227.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEMIP	ENST00000394685.8 linkuse as main transcript	c.2589C>T	p.Ser863=	synonymous_variant	21/30	1	NM_001293298.2	ENSP00000378177	P1	Q8WUJ3-1
CEMIP	ENST00000220244.7 linkuse as main transcript	c.2589C>T	p.Ser863=	synonymous_variant	20/29	1		ENSP00000220244	P1	Q8WUJ3-1
CEMIP	ENST00000356249.9 linkuse as main transcript	c.2589C>T	p.Ser863=	synonymous_variant	21/30	1		ENSP00000348583	P1	Q8WUJ3-1

Frequencies

GnomAD3 genomes

AF:

0.0240

AC:

3643

AN:

152104

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0281

Gnomad AMI

AF:

0.0581

Gnomad AMR

AF:

0.0193

Gnomad ASJ

AF:

0.0282

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.0163

Gnomad MID

AF:

0.0764

Gnomad NFE

AF:

0.0258

Gnomad OTH

AF:

0.0344

GnomAD3 exomes

AF:

0.0195

AC:

4909

AN:

251488

Hom.:

AF XY:

0.0194

AC XY:

2643

AN XY:

135918

show subpopulations

Gnomad AFR exome

AF:

0.0314

Gnomad AMR exome

AF:

0.0145

Gnomad ASJ exome

AF:

0.0268

Gnomad EAS exome

AF:

0.000217

Gnomad SAS exome

AF:

0.00385

Gnomad FIN exome

AF:

0.0202

Gnomad NFE exome

AF:

0.0257

Gnomad OTH exome

AF:

0.0239

GnomAD4 exome

AF:

0.0215

AC:

31451

AN:

1461878

Hom.:

366

Cov.:

AF XY:

0.0211

AC XY:

15371

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.0285

Gnomad4 AMR exome

AF:

0.0157

Gnomad4 ASJ exome

AF:

0.0273

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.00412

Gnomad4 FIN exome

AF:

0.0187

Gnomad4 NFE exome

AF:

0.0236

Gnomad4 OTH exome

AF:

0.0210

GnomAD4 genome

AF:

0.0240

AC:

3647

AN:

152222

Hom.:

Cov.:

AF XY:

0.0222

AC XY:

1651

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.0281

Gnomad4 AMR

AF:

0.0192

Gnomad4 ASJ

AF:

0.0282

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.00207

Gnomad4 FIN

AF:

0.0163

Gnomad4 NFE

AF:

0.0258

Gnomad4 OTH

AF:

0.0341

Alfa

AF:

0.0239

Hom.:

Bravo

AF:

0.0237

Asia WGS

AF:

0.00577

AC:

AN:

3478

EpiCase

AF:

0.0288

EpiControl

AF:

0.0277

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Athena Diagnostics

Feb 03, 2020

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

CEMIP-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Dec 16, 2019

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

-0.84

CADD

Benign

0.74

DANN

Benign

0.83

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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.

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