rs906428

chr15-80850733-G-T

Variant summary

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

The NM_001293298.2(CEMIP):c.-175-22805G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,194 control chromosomes in the GnomAD database, including 1,556 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 0.13 (1556 hom., cov: 32)
• Consequence: CEMIP NM_001293298.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEMIP	NM_001293298.2	c.-175-22805G>T		intron_variant		ENST00000394685.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEMIP	ENST00000394685.8	c.-175-22805G>T		intron_variant		1	NM_001293298.2	P1
CEMIP	ENST00000220244.7	c.-16-23131G>T		intron_variant		1		P1
CEMIP	ENST00000356249.9	c.-115-22805G>T		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19259 AN: 152076 Hom.: 1554 Cov.: 32

Gnomad AFR AF: 0.0327

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.127 AC: 19265 AN: 152194 Hom.: 1556 Cov.: 32 AF XY: 0.125 AC XY: 9309 AN XY: 74412

Gnomad4 AFR AF: 0.0326

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.0850

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.113

Alfa AF: 0.158 Hom.: 2727

Bravo AF: 0.129

Asia WGS AF: 0.159 AC: 555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.3
Dann	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs906428; hg19: chr15-81143074;