9-71685395-TAAAAAAA-TAAAAAAAAAAAAAAA

Variant summary

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

The NM_013390.3(CEMIP2):c.3956-3_3956-2insTTTTTTTT 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 0.00068 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00023 (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_3956-2insTTTTTTTT		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_3956-2insTTTTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_013390.3	P1

Frequencies

GnomAD3 genomes AF: 0.000680 AC: 79 AN: 116094 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00134

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000469

Gnomad ASJ AF: 0.000325

Gnomad EAS AF: 0.00167

Gnomad SAS AF: 0.000285

Gnomad FIN AF: 0.000532

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000388

Gnomad OTH AF: 0.000652

GnomAD4 exome AF: 0.000234 AC: 249 AN: 1062252 Hom.: 0 Cov.: 14 AF XY: 0.000248 AC XY: 126 AN XY: 507716

Gnomad4 AFR exome AF: 0.000405

Gnomad4 AMR exome AF: 0.00139

Gnomad4 ASJ exome AF: 0.000332

Gnomad4 EAS exome AF: 0.000650

Gnomad4 SAS exome AF: 0.00218

Gnomad4 FIN exome AF: 0.000331

Gnomad4 NFE exome AF: 0.000124

Gnomad4 OTH exome AF: 0.000324

GnomAD4 genome AF: 0.000681 AC: 79 AN: 116070 Hom.: 0 Cov.: 0 AF XY: 0.000778 AC XY: 42 AN XY: 53970

Gnomad4 AFR AF: 0.00134

Gnomad4 AMR AF: 0.000469

Gnomad4 ASJ AF: 0.000325

Gnomad4 EAS AF: 0.00168

Gnomad4 SAS AF: 0.000287

Gnomad4 FIN AF: 0.000532

Gnomad4 NFE AF: 0.000388

Gnomad4 OTH AF: 0.000649

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;