GeneBe

NM_013390.3:c.3956-8_3956-3delTTTTTT

Variant names:

Variant summary

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

The NM_013390.3(CEMIP2):​c.3956-8_3956-3delTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000471 in 1,062,530 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: not found (cov: 0)
Exomes 𝑓: 0.0000047 ( 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]

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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;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CEMIP2NM_013390.3 linkc.3956-8_3956-3delTTTTTT splice_region_variant, intron_variant Intron 23 of 23 ENST00000377044.9 NP_037522.1 Q9UHN6-1A0A024R229

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CEMIP2ENST00000377044.9 linkc.3956-8_3956-3delTTTTTT splice_region_variant, intron_variant Intron 23 of 23 1 NM_013390.3 ENSP00000366243.4 Q9UHN6-1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000471
AC:
5
AN:
1062530
Hom.:
0
AF XY:
0.00000591
AC XY:
3
AN XY:
507878
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
22248
American (AMR)
AF:
0.00
AC:
0
AN:
11544
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
15040
East Asian (EAS)
AF:
0.0000382
AC:
1
AN:
26194
South Asian (SAS)
AF:
0.0000320
AC:
1
AN:
31242
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
24172
Middle Eastern (MID)
AF:
0.000339
AC:
1
AN:
2954
European-Non Finnish (NFE)
AF:
0.00000226
AC:
2
AN:
885904
Other (OTH)
AF:
0.00
AC:
0
AN:
43232
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.445
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<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
Cov.:
0
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
3.0

Splicing

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

Publications

Other links and lift over

dbSNP: rs36080695; hg19: chr9-74300311; API