Variant 9-71685395-T-TAAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NM_013390.3(CEMIP2):c.3956-3_3956-2insTTT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.023 ( 54 hom., cov: 0)

Exomes 𝑓: 0.039 ( 34 hom. )

Consequence

CEMIP2
NM_013390.3 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign/Likely benign no assertion criteria provided B:2

Conservation

PhyloP100: 0.302

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 -9 ACMG points.

BP6

Variant 9-71685395-T-TAAA is Benign according to our data. Variant chr9-71685395-T-TAAA is described in ClinVar as [Likely_benign]. Clinvar id is 1206164.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0976 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.3956-3_3956-2insTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000377044.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEMIP2	ENST00000377044.9 linkuse as main transcript	c.3956-3_3956-2insTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_013390.3	P1	Q9UHN6-1

Frequencies

GnomAD3 genomes

AF:

0.0233

AC:

2713

AN:

116248

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0390

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0107

Gnomad ASJ

AF:

0.0315

Gnomad EAS

AF:

0.00641

Gnomad SAS

AF:

0.0439

Gnomad FIN

AF:

0.00852

Gnomad MID

AF:

0.0259

Gnomad NFE

AF:

0.0189

Gnomad OTH

AF:

0.0170

GnomAD3 exomes

AF:

0.0430

AC:

763

AN:

17724

Hom.:

AF XY:

0.0453

AC XY:

426

AN XY:

9410

show subpopulations

Gnomad AFR exome

AF:

0.0821

Gnomad AMR exome

AF:

0.0522

Gnomad ASJ exome

AF:

0.0366

Gnomad EAS exome

AF:

0.0836

Gnomad SAS exome

AF:

0.0604

Gnomad FIN exome

AF:

0.0152

Gnomad NFE exome

AF:

0.0276

Gnomad OTH exome

AF:

0.0461

GnomAD4 exome

AF:

0.0386

AC:

40100

AN:

1039446

Hom.:

Cov.:

AF XY:

0.0384

AC XY:

19084

AN XY:

496616

show subpopulations

Gnomad4 AFR exome

AF:

0.101

Gnomad4 AMR exome

AF:

0.0350

Gnomad4 ASJ exome

AF:

0.0286

Gnomad4 EAS exome

AF:

0.0494

Gnomad4 SAS exome

AF:

0.0627

Gnomad4 FIN exome

AF:

0.0308

Gnomad4 NFE exome

AF:

0.0363

Gnomad4 OTH exome

AF:

0.0386

GnomAD4 genome

AF:

0.0234

AC:

2714

AN:

116224

Hom.:

Cov.:

AF XY:

0.0228

AC XY:

1232

AN XY:

54034

show subpopulations

Gnomad4 AFR

AF:

0.0391

Gnomad4 AMR

AF:

0.0107

Gnomad4 ASJ

AF:

0.0315

Gnomad4 EAS

AF:

0.00644

Gnomad4 SAS

AF:

0.0440

Gnomad4 FIN

AF:

0.00852

Gnomad4 NFE

AF:

0.0189

Gnomad4 OTH

AF:

0.0169

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, no assertion criteria provided

clinical testing

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

- -

not provided

Benign:1

Likely benign, no assertion criteria provided

clinical testing

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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