chr15-80880637-C-T

Position:

• chr15-80880637-C-T

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.381-263C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,092 control chromosomes in the GnomAD database, including 2,318 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.17 (2318 hom., cov: 32)
• Consequence: CEMIP NM_001293298.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.50

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=-0.99).
• BP6: Variant 15-80880637-C-T is Benign according to our data. Variant chr15-80880637-C-T is described in ClinVar as [Benign]. Clinvar id is 1244735.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEMIP	NM_001293298.2	c.381-263C>T		intron_variant		ENST00000394685.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEMIP	ENST00000394685.8	c.381-263C>T		intron_variant		1	NM_001293298.2	P1
CEMIP	ENST00000220244.7	c.381-263C>T		intron_variant		1		P1
CEMIP	ENST00000356249.9	c.381-263C>T		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25137 AN: 151974 Hom.: 2312 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.0878

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.165 AC: 25161 AN: 152092 Hom.: 2318 Cov.: 32 AF XY: 0.169 AC XY: 12544 AN XY: 74346

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.0878

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.148

Alfa AF: 0.161 Hom.: 252

Bravo AF: 0.167

Asia WGS AF: 0.235 AC: 815 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	-0.99
CADD	Benign	3.1
DANN	Benign	0.77

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: rs9673075; hg19: chr15-81172978; COSMIC: COSV55000895;