Variant rs3739783 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_013390.3(CEMIP2):c.759C>G(p.Pro253=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 1,613,844 control chromosomes in the GnomAD database, including 15,717 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.12 ( 1253 hom., cov: 31)

Exomes 𝑓: 0.14 ( 14464 hom. )

Consequence

CEMIP2
NM_013390.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.550

Variant links:

Genes affected

CEMIP2 (HGNC:11869): (cell migration inducing hyaluronidase 2) This gene encodes a type II transmembrane protein that belongs to the interferon-induced transmembrane (IFITM) protein superfamily. The encoded protein functions as a cell surface hyaluronidase that cleaves extracellular high molecular weight hyaluronan into intermediate size fragments before internalization and degradation in the lysosome. It also has an interferon-mediated antiviral function in humans through activation of the JAK STAT signaling pathway. The activation of this gene by transcription factor SOX4 in breast cancer cells has been shown to mediate the pathological effects of SOX4 on cancer progression. Naturally occurring mutations in this gene are associated with autosomal recessive non-syndromic hearing loss. [provided by RefSeq, Mar 2017]

CEMIP2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP7

Synonymous conserved (PhyloP=0.55 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEMIP2	NM_013390.3 linkuse as main transcript	c.759C>G	p.Pro253=	synonymous_variant	4/24	ENST00000377044.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEMIP2	ENST00000377044.9 linkuse as main transcript	c.759C>G	p.Pro253=	synonymous_variant	4/24	1	NM_013390.3	P1	Q9UHN6-1
CEMIP2	ENST00000377066.9 linkuse as main transcript	c.759C>G	p.Pro253=	synonymous_variant	4/23	1			Q9UHN6-2
CEMIP2	ENST00000542935.5 linkuse as main transcript	c.759C>G	p.Pro253=	synonymous_variant, NMD_transcript_variant	4/24	1

Frequencies

GnomAD3 genomes

AF:

0.117

AC:

17745

AN:

151994

Hom.:

1248

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0458

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.164

Gnomad ASJ

AF:

0.134

Gnomad EAS

AF:

0.157

Gnomad SAS

AF:

0.158

Gnomad FIN

AF:

0.185

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.132

Gnomad OTH

AF:

0.115

GnomAD3 exomes

AF:

0.145

AC:

36315

AN:

251222

Hom.:

2874

AF XY:

0.145

AC XY:

19642

AN XY:

135780

show subpopulations

Gnomad AFR exome

AF:

0.0447

Gnomad AMR exome

AF:

0.198

Gnomad ASJ exome

AF:

0.139

Gnomad EAS exome

AF:

0.158

Gnomad SAS exome

AF:

0.149

Gnomad FIN exome

AF:

0.179

Gnomad NFE exome

AF:

0.134

Gnomad OTH exome

AF:

0.129

GnomAD4 exome

AF:

0.138

AC:

201326

AN:

1461732

Hom.:

14464

Cov.:

AF XY:

0.138

AC XY:

100372

AN XY:

727132

show subpopulations

Gnomad4 AFR exome

AF:

0.0387

Gnomad4 AMR exome

AF:

0.191

Gnomad4 ASJ exome

AF:

0.139

Gnomad4 EAS exome

AF:

0.141

Gnomad4 SAS exome

AF:

0.150

Gnomad4 FIN exome

AF:

0.181

Gnomad4 NFE exome

AF:

0.136

Gnomad4 OTH exome

AF:

0.132

GnomAD4 genome

AF:

0.117

AC:

17748

AN:

152112

Hom.:

1253

Cov.:

AF XY:

0.121

AC XY:

9007

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.0456

Gnomad4 AMR

AF:

0.164

Gnomad4 ASJ

AF:

0.134

Gnomad4 EAS

AF:

0.157

Gnomad4 SAS

AF:

0.159

Gnomad4 FIN

AF:

0.185

Gnomad4 NFE

AF:

0.132

Gnomad4 OTH

AF:

0.113

Alfa

AF:

0.127

Hom.:

426

Bravo

AF:

0.111

Asia WGS

AF:

0.128

AC:

444

AN:

3478

EpiCase

AF:

0.127

EpiControl

AF:

0.132

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.0

DANN

Benign

0.43

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over