rs10152744

Variant names:

• chr15-80879449-G-C
• rs10152744
• NM_001293298.2:c.242-267G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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]

CEMIP Gene-Disease associations (from GenCC):

• nonsyndromic genetic hearing loss

  Inheritance: AR Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001293298.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEMIP	NM_001293298.2	MANE Select	c.242-267G>C		intron	N/A	NP_001280227.1	Q8WUJ3-1
	CEMIP	NM_001293304.2		c.242-267G>C		intron	N/A	NP_001280233.1	Q8WUJ3-1
	CEMIP	NM_018689.3		c.242-267G>C		intron	N/A	NP_061159.1	Q8WUJ3-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEMIP	ENST00000394685.8	TSL:1 MANE Select	c.242-267G>C		intron	N/A	ENSP00000378177.3	Q8WUJ3-1
	CEMIP	ENST00000220244.7	TSL:1	c.242-267G>C		intron	N/A	ENSP00000220244.3	Q8WUJ3-1
	CEMIP	ENST00000356249.9	TSL:1	c.242-267G>C		intron	N/A	ENSP00000348583.5	Q8WUJ3-1

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

African (AFR) AF: 0.231 AC: 9581 AN: 41490

American (AMR) AF: 0.375 AC: 5732 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1090 AN: 3466

East Asian (EAS) AF: 0.582 AC: 3014 AN: 5176

South Asian (SAS) AF: 0.367 AC: 1766 AN: 4808

European-Finnish (FIN) AF: 0.324 AC: 3424 AN: 10568

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18202 AN: 67992

Other (OTH) AF: 0.333 AC: 702 AN: 2110

Alfa AF: 0.268 Hom.: 708

Bravo AF: 0.290

Asia WGS AF: 0.468 AC: 1625 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.52
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10152744; hg19: chr15-81171790;