9-71685395-TAAAAAAA-TAAAAAAAAAAAAA

Position:

• chr9-71685395-TAAAAAAA-TAAAAAAAAAAAAA

Variant summary

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

The NM_013390.3(CEMIP2):​c.3956-3_3956-2insTTTTTT variant causes a splice region, splice polypyrimidine tract, 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 0.000086 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00020 (0 hom.)
• Consequence: CEMIP2 NM_013390.3 splice_region, splice_polypyrimidine_tract, 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/exons	MANE	UniProt
CEMIP2	NM_013390.3	c.3956-3_3956-2insTTTTTT		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	c.3956-3_3956-2insTTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_013390.3	P1

Frequencies

GnomAD3 genomes AF: 0.0000860 AC: 10 AN: 116308 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000684

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: 0.000266

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000118

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000203 AC: 216 AN: 1062272 Hom.: 0 Cov.: 14 AF XY: 0.000234 AC XY: 119 AN XY: 507752

Gnomad4 AFR exome AF: 0.000225

Gnomad4 AMR exome AF: 0.000867

Gnomad4 ASJ exome AF: 0.000666

Gnomad4 EAS exome AF: 0.000306

Gnomad4 SAS exome AF: 0.00167

Gnomad4 FIN exome AF: 0.000414

Gnomad4 NFE exome AF: 0.000122

Gnomad4 OTH exome AF: 0.000278

GnomAD4 genome AF: 0.0000860 AC: 10 AN: 116284 Hom.: 0 Cov.: 0 AF XY: 0.0000740 AC XY: 4 AN XY: 54066

Gnomad4 AFR AF: 0.0000683

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000266

Gnomad4 NFE AF: 0.000118

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;