rs16972342

chr15-80783457-T-Achr15-80783457-T-G

Variant summary

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

The NM_001293298.2(CEMIP):c.-176+3843T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0583 in 152,276 control chromosomes in the GnomAD database, including 652 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 0.058 (652 hom., cov: 33)
• Consequence: CEMIP NM_001293298.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.635

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEMIP	NM_001293298.2	c.-176+3843T>A		intron_variant		ENST00000394685.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEMIP	ENST00000394685.8	c.-176+3843T>A		intron_variant		1	NM_001293298.2	P1
CEMIP	ENST00000220244.7	c.-17+3843T>A		intron_variant		1		P1
CEMIP	ENST00000356249.9	c.-116+3843T>A		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.0584 AC: 8890 AN: 152158 Hom.: 653 Cov.: 33

Gnomad AFR AF: 0.0125

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.0769

Gnomad ASJ AF: 0.0631

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0405

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0509

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0583 AC: 8882 AN: 152276 Hom.: 652 Cov.: 33 AF XY: 0.0624 AC XY: 4647 AN XY: 74448

Gnomad4 AFR AF: 0.0125

Gnomad4 AMR AF: 0.0767

Gnomad4 ASJ AF: 0.0631

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.0405

Gnomad4 NFE AF: 0.0510

Gnomad4 OTH AF: 0.0591

Alfa AF: 0.0467 Hom.: 39

Bravo AF: 0.0596

Asia WGS AF: 0.286 AC: 993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	8.4
Dann	Benign	0.72

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: rs16972342; hg19: chr15-81075798;