9-71685395-TAAAAAAA-TAAAAAAAAAAAAAAAAAAAAA

Position:

• chr9-71685395-TAAAAAAA-TAAAAAAAAAAAAAAAAAAAAA

Variant summary

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

The NM_013390.3(CEMIP2):​c.3956-16_3956-3dupTTTTTTTTTTTTTT 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 0.000026 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000018 (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]

CEMIP2 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEMIP2	NM_013390.3	c.3956-16_3956-3dupTTTTTTTTTTTTTT		splice_region_variant, intron_variant		ENST00000377044.9	NP_037522.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEMIP2	ENST00000377044.9	c.3956-16_3956-3dupTTTTTTTTTTTTTT		splice_region_variant, intron_variant		1	NM_013390.3	ENSP00000366243.4

Frequencies

GnomAD3 genomes AF: 0.0000258 AC: 3 AN: 116356 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000684

Gnomad AMI AF: 0.00122

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: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000179 AC: 19 AN: 1062546 Hom.: 0 Cov.: 14 AF XY: 0.0000236 AC XY: 12 AN XY: 507886

Gnomad4 AFR exome AF: 0.0000449

Gnomad4 AMR exome AF: 0.0000866

Gnomad4 ASJ exome AF: 0.0000665

Gnomad4 EAS exome AF: 0.000115

Gnomad4 SAS exome AF: 0.0000960

Gnomad4 FIN exome AF: 0.0000414

Gnomad4 NFE exome AF: 0.00000903

Gnomad4 OTH exome AF: 0.0000231

GnomAD4 genome AF: 0.0000258 AC: 3 AN: 116356 Hom.: 0 Cov.: 0 AF XY: 0.0000370 AC XY: 2 AN XY: 54086

Gnomad4 AFR AF: 0.0000684

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

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;