chr15-80878590-G-A

Position:

• chr15-80878590-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000394685.8(CEMIP):​c.95-131G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00886 in 1,168,966 control chromosomes in the GnomAD database, including 460 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.035 (282 hom., cov: 33)
  • Exomes 𝑓: 0.0050 (178 hom.)
• Consequence: CEMIP ENST00000394685.8 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0810

Genes affected

CEMIP (HGNC:29213): (cell migration inducing hyaluronidase 1) Enables several functions, including clathrin heavy chain binding activity; hyaluronic acid binding activity; and hyalurononglucosaminidase activity. Involved in several processes, including hyaluronan catabolic process; positive regulation of protein phosphorylation; and positive regulation of transport. Located in clathrin-coated endocytic vesicle; endoplasmic reticulum; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 15-80878590-G-A is Benign according to our data. Variant chr15-80878590-G-A is described in ClinVar as [Benign]. Clinvar id is 1281219.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEMIP	NM_001293298.2	c.95-131G>A		intron_variant		ENST00000394685.8	NP_001280227.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEMIP	ENST00000394685.8	c.95-131G>A		intron_variant		1	NM_001293298.2	ENSP00000378177	P1
CEMIP	ENST00000220244.7	c.95-131G>A		intron_variant		1		ENSP00000220244	P1
CEMIP	ENST00000356249.9	c.95-131G>A		intron_variant		1		ENSP00000348583	P1

Frequencies

GnomAD3 genomes AF: 0.0347 AC: 5276 AN: 152174 Hom.: 277 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0185

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00195

Gnomad OTH AF: 0.0263

GnomAD4 exome AF: 0.00498 AC: 5063 AN: 1016674 Hom.: 178 AF XY: 0.00431 AC XY: 2238 AN XY: 518796

Gnomad4 AFR exome AF: 0.115

Gnomad4 AMR exome AF: 0.0103

Gnomad4 ASJ exome AF: 0.00177

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000404

Gnomad4 FIN exome AF: 0.0000491

Gnomad4 NFE exome AF: 0.00177

Gnomad4 OTH exome AF: 0.0103

GnomAD4 genome AF: 0.0348 AC: 5298 AN: 152292 Hom.: 282 Cov.: 33 AF XY: 0.0340 AC XY: 2534 AN XY: 74466

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0182

Gnomad4 ASJ AF: 0.00115

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000415

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00195

Gnomad4 OTH AF: 0.0260

Alfa AF: 0.000585 Hom.: 0

Bravo AF: 0.0398

Asia WGS AF: 0.00491 AC: 18 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 21, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.32

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs73501087; hg19: chr15-81170931;