15-80879449-G-C

Position:

• chr15-80879449-G-C

Variant summary

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

The NM_001293298.2(CEMIP):​c.242-267G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,098 control chromosomes in the GnomAD database, including 6,859 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.29 (6859 hom., cov: 33)
• Consequence: CEMIP NM_001293298.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.19

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=-0.96).
• BP6: Variant 15-80879449-G-C is Benign according to our data. Variant chr15-80879449-G-C is described in ClinVar as [Benign]. Clinvar id is 1268997.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEMIP	NM_001293298.2	c.242-267G>C		intron_variant		ENST00000394685.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEMIP	ENST00000394685.8	c.242-267G>C		intron_variant		1	NM_001293298.2	P1
CEMIP	ENST00000220244.7	c.242-267G>C		intron_variant		1		P1
CEMIP	ENST00000356249.9	c.242-267G>C		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43759 AN: 151980 Hom.: 6848 Cov.: 33

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.331

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.288 AC: 43798 AN: 152098 Hom.: 6859 Cov.: 33 AF XY: 0.297 AC XY: 22081 AN XY: 74352

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.333

Alfa AF: 0.268 Hom.: 708

Bravo AF: 0.290

Asia WGS AF: 0.468 AC: 1625 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

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs10152744; hg19: chr15-81171790;