9-71685395-TAAAAAAA-TAAAAAAAAAAA

Position:

• chr9-71685395-TAAAAAAA-TAAAAAAAAAAA

Variant summary

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

The NM_013390.3(CEMIP2):​c.3956-6_3956-3dupTTTT 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 0.00015 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0027 (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.3956-6_3956-3dupTTTT		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.3956-6_3956-3dupTTTT		splice_region_variant, intron_variant		1	NM_013390.3	ENSP00000366243.4

Frequencies

GnomAD3 genomes AF: 0.000138 AC: 16 AN: 116348 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: 0.000237

Gnomad SAS AF: 0.000285

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000169

Gnomad OTH AF: 0.00130

GnomAD3 exomes AF: 0.00824 AC: 146 AN: 17724 Hom.: 1 AF XY: 0.00786 AC XY: 74 AN XY: 9410

Gnomad AFR exome AF: 0.0113

Gnomad AMR exome AF: 0.00611

Gnomad ASJ exome AF: 0.00762

Gnomad EAS exome AF: 0.0154

Gnomad SAS exome AF: 0.00883

Gnomad FIN exome AF: 0.00351

Gnomad NFE exome AF: 0.00738

Gnomad OTH exome AF: 0.0110

GnomAD4 exome AF: 0.00274 AC: 2905 AN: 1058464 Hom.: 1 Cov.: 14 AF XY: 0.00270 AC XY: 1365 AN XY: 505974

Gnomad4 AFR exome AF: 0.00673

Gnomad4 AMR exome AF: 0.00339

Gnomad4 ASJ exome AF: 0.00300

Gnomad4 EAS exome AF: 0.00203

Gnomad4 SAS exome AF: 0.00863

Gnomad4 FIN exome AF: 0.00203

Gnomad4 NFE exome AF: 0.00247

Gnomad4 OTH exome AF: 0.00274

GnomAD4 genome AF: 0.000155 AC: 18 AN: 116324 Hom.: 0 Cov.: 0 AF XY: 0.000203 AC XY: 11 AN XY: 54084

Gnomad4 AFR AF: 0.0000683

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000238

Gnomad4 SAS AF: 0.000287

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000169

Gnomad4 OTH AF: 0.00260

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;