rs748696

chr15-80801547-G-Achr15-80801547-G-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+21933G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,114 control chromosomes in the GnomAD database, including 10,775 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 0.36 (10775 hom., cov: 33)
• Consequence: CEMIP NM_001293298.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEMIP	NM_001293298.2	c.-176+21933G>A		intron_variant		ENST00000394685.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEMIP	ENST00000394685.8	c.-176+21933G>A		intron_variant		1	NM_001293298.2	P1
CEMIP	ENST00000220244.7	c.-17+21933G>A		intron_variant		1		P1
CEMIP	ENST00000356249.9	c.-116+21933G>A		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54253 AN: 151996 Hom.: 10776 Cov.: 33

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.357 AC: 54249 AN: 152114 Hom.: 10775 Cov.: 33 AF XY: 0.354 AC XY: 26302 AN XY: 74364

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.340

Alfa AF: 0.426 Hom.: 29806

Bravo AF: 0.337

Asia WGS AF: 0.203 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	6.9
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: rs748696; hg19: chr15-81093888;