9-5841438-G-A

Variant names:

• chr9-5841438-G-A
• rs7047575
• XM_017015139.3:c.153-10410C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000690753.1(ERMP1):​n.3200-8126C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 152,002 control chromosomes in the GnomAD database, including 17,438 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 0.48 (17438 hom., cov: 32)
• Consequence: ERMP1 ENST00000690753.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000690753.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERMP1	ENST00000690753.1		n.3200-8126C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72260 AN: 151884 Hom.: 17433 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.476 AC: 72297 AN: 152002 Hom.: 17438 Cov.: 32 AF XY: 0.475 AC XY: 35268 AN XY: 74312

African (AFR) AF: 0.413 AC: 17095 AN: 41442

American (AMR) AF: 0.460 AC: 7022 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1717 AN: 3470

East Asian (EAS) AF: 0.243 AC: 1259 AN: 5174

South Asian (SAS) AF: 0.523 AC: 2520 AN: 4822

European-Finnish (FIN) AF: 0.521 AC: 5500 AN: 10566

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35554 AN: 67940

Other (OTH) AF: 0.478 AC: 1005 AN: 2104

Alfa AF: 0.498 Hom.: 34755

Bravo AF: 0.466

Asia WGS AF: 0.385 AC: 1343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.63
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs7047575; hg19: chr9-5841438;