chr9-5830317-T-C

Variant names:

• chr9-5830317-T-C
• rs17571216
• NM_024896.3:c.640+410A>G

Variant summary

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

The NM_024896.3(ERMP1):​c.640+410A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,988 control chromosomes in the GnomAD database, including 10,256 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 0.34 (10256 hom., cov: 31)
• Consequence: ERMP1 NM_024896.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ERMP1	NM_024896.3	c.640+410A>G		intron_variant	Intron 2 of 14	ENST00000339450.10	NP_079172.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ERMP1	ENST00000339450.10	c.640+410A>G		intron_variant	Intron 2 of 14	1	NM_024896.3	ENSP00000340427.5

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51803 AN: 151870 Hom.: 10251 Cov.: 31

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.341 AC: 51832 AN: 151988 Hom.: 10256 Cov.: 31 AF XY: 0.352 AC XY: 26169 AN XY: 74292

African (AFR) AF: 0.173 AC: 7170 AN: 41472

American (AMR) AF: 0.431 AC: 6577 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1217 AN: 3472

East Asian (EAS) AF: 0.753 AC: 3887 AN: 5160

South Asian (SAS) AF: 0.532 AC: 2557 AN: 4810

European-Finnish (FIN) AF: 0.450 AC: 4750 AN: 10554

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24438 AN: 67936

Other (OTH) AF: 0.360 AC: 759 AN: 2110

Alfa AF: 0.349 Hom.: 1298

Bravo AF: 0.330

Asia WGS AF: 0.591 AC: 2055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.33
DANN	Benign	0.70
PhyloP100		-0.64
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17571216; hg19: chr9-5830317;