rs10758713

chr9-5872949-A-G

Variant summary

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

The ENST00000690753.1(ERMP1):n.2896-733T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.905 in 152,148 control chromosomes in the GnomAD database, including 62,575 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 0.91 (62575 hom., cov: 31)
• Consequence: ERMP1 ENST00000690753.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

ERMP1 (HGNC:23703): (endoplasmic reticulum metallopeptidase 1) Predicted to enable metal ion binding activity and metalloexopeptidase activity. Involved in cellular response to oxidative stress. Acts upstream of or within endoplasmic reticulum unfolded protein response. Located in 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ERMP1	ENST00000690753.1	n.2896-733T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.905 AC: 137618 AN: 152030 Hom.: 62508 Cov.: 31

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.905 AC: 137745 AN: 152148 Hom.: 62575 Cov.: 31 AF XY: 0.902 AC XY: 67062 AN XY: 74370

Gnomad4 AFR AF: 0.956

Gnomad4 AMR AF: 0.902

Gnomad4 ASJ AF: 0.827

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.805

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.902

Gnomad4 OTH AF: 0.885

Alfa AF: 0.895 Hom.: 72171

Bravo AF: 0.909

Asia WGS AF: 0.744 AC: 2590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.48

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10758713; hg19: chr9-5872949; COSMIC: COSV69444546;