9-111371352-T-C

Variant names:

• chr9-111371352-T-C
• rs2282181
• NM_001364929.1:c.4737+269A>G

Variant summary

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

The NM_001364929.1(ECPAS):​c.4737+269A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0557 in 152,188 control chromosomes in the GnomAD database, including 571 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 0.056 (571 hom., cov: 32)
• Consequence: ECPAS NM_001364929.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 2 publications found

Genes affected

ECPAS (HGNC:29020): (Ecm29 proteasome adaptor and scaffold) Enables proteasome binding activity. Involved in ubiquitin-dependent ERAD pathway. Located in several cellular components, including centrosome; cytoplasmic vesicle; and nucleoplasm. [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 (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001364929.1. 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
	ECPAS	NM_001364929.1	MANE Select	c.4737+269A>G		intron	N/A	NP_001351858.1
	ECPAS	NM_001364931.1		c.4755+269A>G		intron	N/A	NP_001351860.1
	ECPAS	NM_001363756.2		c.4737+269A>G		intron	N/A	NP_001350685.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ECPAS	ENST00000684092.1	MANE Select	c.4737+269A>G		intron	N/A	ENSP00000507419.1
	ECPAS	ENST00000259335.8	TSL:1	c.5271+269A>G		intron	N/A	ENSP00000259335.4
	ECPAS	ENST00000338205.9	TSL:5	c.4737+269A>G		intron	N/A	ENSP00000339889.5

Frequencies

GnomAD3 genomes AF: 0.0556 AC: 8457 AN: 152070 Hom.: 568 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0257

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.0340

Gnomad FIN AF: 0.00188

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0118

Gnomad OTH AF: 0.0508

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

GnomAD4 genome AF: 0.0557 AC: 8477 AN: 152188 Hom.: 571 Cov.: 32 AF XY: 0.0541 AC XY: 4026 AN XY: 74402

African (AFR) AF: 0.149 AC: 6185 AN: 41484

American (AMR) AF: 0.0257 AC: 393 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3472

East Asian (EAS) AF: 0.143 AC: 740 AN: 5178

South Asian (SAS) AF: 0.0340 AC: 164 AN: 4818

European-Finnish (FIN) AF: 0.00188 AC: 20 AN: 10618

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0118 AC: 803 AN: 68006

Other (OTH) AF: 0.0502 AC: 106 AN: 2110

Alfa AF: 0.0408 Hom.: 76

Bravo AF: 0.0630

Asia WGS AF: 0.0900 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.057
DANN	Benign	0.32
PhyloP100		-2.5
PromoterAI		0.028	Neutral
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: rs2282181; hg19: chr9-114133632;