9-5807444-T-G

Variant names:

• chr9-5807444-T-G
• rs2797512
• NM_024896.3:c.1549-1659A>C

Variant summary

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

The NM_024896.3(ERMP1):​c.1549-1659A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0578 in 152,130 control chromosomes in the GnomAD database, including 814 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 (814 hom., cov: 31)
• Consequence: ERMP1 NM_024896.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024896.3. 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
	ERMP1	NM_024896.3	MANE Select	c.1549-1659A>C		intron	N/A	NP_079172.2
	ERMP1	NM_001410952.1		c.1548+2567A>C		intron	N/A	NP_001397881.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERMP1	ENST00000339450.10	TSL:1 MANE Select	c.1549-1659A>C		intron	N/A	ENSP00000340427.5
	ERMP1	ENST00000214893.10	TSL:1	n.975-1659A>C		intron	N/A
	ERMP1	ENST00000489219.5	TSL:1	n.1549-1659A>C		intron	N/A	ENSP00000417474.1

Frequencies

GnomAD3 genomes AF: 0.0576 AC: 8757 AN: 152012 Hom.: 813 Cov.: 31

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0269

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000830

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00190

Gnomad OTH AF: 0.0480

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

GnomAD4 genome AF: 0.0578 AC: 8791 AN: 152130 Hom.: 814 Cov.: 31 AF XY: 0.0562 AC XY: 4178 AN XY: 74376

African (AFR) AF: 0.195 AC: 8074 AN: 41442

American (AMR) AF: 0.0269 AC: 411 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0161 AC: 56 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.000831 AC: 4 AN: 4816

European-Finnish (FIN) AF: 0.0000942 AC: 1 AN: 10618

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.00190 AC: 129 AN: 68014

Other (OTH) AF: 0.0480 AC: 101 AN: 2104

Alfa AF: 0.0220 Hom.: 766

Bravo AF: 0.0668

Asia WGS AF: 0.0120 AC: 42 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.74
PhyloP100		-0.72
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2797512; hg19: chr9-5807444;