9-71685395-TAAAAAAA-TAAAAAAAAAAAAAA

Position:

• chr9-71685395-TAAAAAAA-TAAAAAAAAAAAAAA

Variant summary

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

The NM_013390.3(CEMIP2):​c.3956-9_3956-3dupTTTTTTT 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 0.00066 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00032 (1 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.3956-9_3956-3dupTTTTTTT		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.3956-9_3956-3dupTTTTTTT		splice_region_variant, intron_variant		1	NM_013390.3	ENSP00000366243.4

Frequencies

GnomAD3 genomes AF: 0.000655 AC: 76 AN: 115946 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000480

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000376

Gnomad ASJ AF: 0.00131

Gnomad EAS AF: 0.00143

Gnomad SAS AF: 0.000285

Gnomad FIN AF: 0.000533

Gnomad MID AF: 0.00439

Gnomad NFE AF: 0.000728

Gnomad OTH AF: 0.000654

GnomAD3 exomes AF: 0.00564 AC: 100 AN: 17724 Hom.: 0 AF XY: 0.00584 AC XY: 55 AN XY: 9410

Gnomad AFR exome AF: 0.00644

Gnomad AMR exome AF: 0.00376

Gnomad ASJ exome AF: 0.0122

Gnomad EAS exome AF: 0.0140

Gnomad SAS exome AF: 0.00325

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00499

Gnomad OTH exome AF: 0.0110

GnomAD4 exome AF: 0.000321 AC: 341 AN: 1062164 Hom.: 1 Cov.: 14 AF XY: 0.000355 AC XY: 180 AN XY: 507688

Gnomad4 AFR exome AF: 0.000360

Gnomad4 AMR exome AF: 0.00122

Gnomad4 ASJ exome AF: 0.000798

Gnomad4 EAS exome AF: 0.000994

Gnomad4 SAS exome AF: 0.00218

Gnomad4 FIN exome AF: 0.000373

Gnomad4 NFE exome AF: 0.000213

Gnomad4 OTH exome AF: 0.000301

GnomAD4 genome AF: 0.000656 AC: 76 AN: 115924 Hom.: 0 Cov.: 0 AF XY: 0.000650 AC XY: 35 AN XY: 53886

Gnomad4 AFR AF: 0.000479

Gnomad4 AMR AF: 0.000376

Gnomad4 ASJ AF: 0.00131

Gnomad4 EAS AF: 0.00143

Gnomad4 SAS AF: 0.000287

Gnomad4 FIN AF: 0.000533

Gnomad4 NFE AF: 0.000728

Gnomad4 OTH AF: 0.000652

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;