9-5841438-G-A

Position:

• chr9-5841438-G-A

Variant summary

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

The XM_017015139.3(ERMP1):​c.153-10410C>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 XM_017015139.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ERMP1	XM_017015139.3	c.153-10410C>T		intron_variant			XP_016870628.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ERMP1	ENST00000690753.1	n.3200-8126C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.478

Alfa AF: 0.504 Hom.: 25204

Bravo AF: 0.466

Asia WGS AF: 0.385 AC: 1343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7047575; hg19: chr9-5841438;