Genetic Variant CEMIP2:c.3956-9_3956-3delTTTTTTT (chr9-71685395-TAAAAAAA-T) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_013390.3(CEMIP2):c.3956-9_3956-3delTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000288 in 1,178,902 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000086 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000031 ( 0 hom. )

Consequence

CEMIP2
NM_013390.3 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.98

Publications

3 publications found

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 was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013390.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CEMIP2	NM_013390.3	MANE Select	c.3956-9_3956-3delTTTTTTT	splice_region intron	N/A	NP_037522.1	Q9UHN6-1
CEMIP2	NM_001135820.2		c.3767-9_3767-3delTTTTTTT	splice_region intron	N/A	NP_001129292.1	Q9UHN6-2
CEMIP2	NM_001349784.2		c.2042-9_2042-3delTTTTTTT	splice_region intron	N/A	NP_001336713.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CEMIP2	ENST00000377044.9	TSL:1 MANE Select	c.3956-9_3956-3delTTTTTTT	splice_region intron	N/A	ENSP00000366243.4	Q9UHN6-1
CEMIP2	ENST00000377066.9	TSL:1	c.3767-9_3767-3delTTTTTTT	splice_region intron	N/A	ENSP00000366266.5	Q9UHN6-2
CEMIP2	ENST00000538669.1	TSL:1	n.1687-9_1687-3delTTTTTTT	splice_region intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00000859

AC:

AN:

116356

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000169

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000311

AC:

AN:

1062546

Hom.:

AF XY:

0.0000158

AC XY:

AN XY:

507886

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

22248

American (AMR)

AF:

0.00

AC:

AN:

11548

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15040

East Asian (EAS)

AF:

0.00

AC:

AN:

26194

South Asian (SAS)

AF:

0.00

AC:

AN:

31244

European-Finnish (FIN)

AF:

0.00

AC:

AN:

24176

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2954

European-Non Finnish (NFE)

AF:

0.0000361

AC:

AN:

885910

Other (OTH)

AF:

0.0000231

AC:

AN:

43232

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.436

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00000859

AC:

AN:

116356

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

54086

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

29244

American (AMR)

AF:

0.00

AC:

AN:

10662

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3084

East Asian (EAS)

AF:

0.00

AC:

AN:

4212

South Asian (SAS)

AF:

0.00

AC:

AN:

3512

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3756

Middle Eastern (MID)

AF:

0.00

AC:

AN:

232

European-Non Finnish (NFE)

AF:

0.0000169

AC:

AN:

59302

Other (OTH)

AF:

0.00

AC:

AN:

1534

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

3.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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9-71685395-TAAAAAAAAAAAAA-TAAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over