15-80793142-T-C

Position:

• chr15-80793142-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001293298.2(CEMIP):​c.-176+13528T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 152,026 control chromosomes in the GnomAD database, including 28,264 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.58 (28264 hom., cov: 31)
• Consequence: CEMIP NM_001293298.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEMIP	NM_001293298.2	c.-176+13528T>C		intron_variant		ENST00000394685.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEMIP	ENST00000394685.8	c.-176+13528T>C		intron_variant		1	NM_001293298.2	P1
CEMIP	ENST00000220244.7	c.-17+13528T>C		intron_variant		1		P1
CEMIP	ENST00000356249.9	c.-116+13528T>C		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88039 AN: 151908 Hom.: 28275 Cov.: 31

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.579 AC: 88033 AN: 152026 Hom.: 28264 Cov.: 31 AF XY: 0.578 AC XY: 42900 AN XY: 74278

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.605

Alfa AF: 0.699 Hom.: 76851

Bravo AF: 0.561

Asia WGS AF: 0.639 AC: 2224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.47

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: rs925111; hg19: chr15-81085483;