NM_013390.3:c.3956-12_3956-3dupTTTTTTTTTT

Variant names:

• chr9-71685395-T-TAAAAAAAAAA
• rs36080695
• NM_013390.3:c.3956-12_3956-3dupTTTTTTTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_013390.3(CEMIP2):​c.3956-12_3956-3dupTTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00029 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00013 (0 hom.)
• Consequence: CEMIP2 NM_013390.3 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEMIP2	NM_013390.3	c.3956-12_3956-3dupTTTTTTTTTT		splice_region_variant, intron_variant	Intron 23 of 23	ENST00000377044.9	NP_037522.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEMIP2	ENST00000377044.9	c.3956-3_3956-2insTTTTTTTTTT		splice_region_variant, intron_variant	Intron 23 of 23	1	NM_013390.3	ENSP00000366243.4

Frequencies

GnomAD3 genomes AF: 0.000292 AC: 34 AN: 116310 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000171

Gnomad AMI AF: 0.00122

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.000649

Gnomad EAS AF: 0.000475

Gnomad SAS AF: 0.000855

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000354

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000133 AC: 141 AN: 1062474 Hom.: 0 Cov.: 14 AF XY: 0.000159 AC XY: 81 AN XY: 507842

Gnomad4 AFR exome AF: 0.000180

Gnomad4 AMR exome AF: 0.000346

Gnomad4 ASJ exome AF: 0.000133

Gnomad4 EAS exome AF: 0.000725

Gnomad4 SAS exome AF: 0.000672

Gnomad4 FIN exome AF: 0.0000414

Gnomad4 NFE exome AF: 0.0000960

Gnomad4 OTH exome AF: 0.000116

GnomAD4 genome AF: 0.000292 AC: 34 AN: 116286 Hom.: 0 Cov.: 0 AF XY: 0.000351 AC XY: 19 AN XY: 54064

Gnomad4 AFR AF: 0.000171

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.000649

Gnomad4 EAS AF: 0.000477

Gnomad4 SAS AF: 0.000861

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000354

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36080695; hg19: chr9-74300311;