2-75493442-CGCTGTCGCT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001135032.2(EVA1A):c.244_252del(p.Ser82_Ser84del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.0471 in 1,614,160 control chromosomes in the GnomAD database, including 2,051 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.052 (242 hom., cov: 32)
  • Exomes 𝑓: 0.047 (1809 hom.)
• Consequence: EVA1A NM_001135032.2 inframe_deletion
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 5.05

Genes affected

EVA1A (HGNC:25816): (eva-1 homolog A, regulator of programmed cell death) Predicted to be involved in apoptotic process and autophagy. Located in intracellular membrane-bounded organelle and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 2-75493442-CGCTGTCGCT-C is Benign according to our data. Variant chr2-75493442-CGCTGTCGCT-C is described in ClinVar as [Benign]. Clinvar id is 3055669.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EVA1A	NM_001135032.2	c.244_252del	p.Ser82_Ser84del	inframe_deletion	4/4	ENST00000393913.8
EVA1A	NM_001369524.1	c.244_252del	p.Ser82_Ser84del	inframe_deletion	6/6
EVA1A	NM_001369525.1	c.244_252del	p.Ser82_Ser84del	inframe_deletion	5/5
EVA1A	NM_032181.3	c.244_252del	p.Ser82_Ser84del	inframe_deletion	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EVA1A	ENST00000393913.8	c.244_252del	p.Ser82_Ser84del	inframe_deletion	4/4	1	NM_001135032.2	P1

Frequencies

GnomAD3 genomes AF: 0.0518 AC: 7881 AN: 152198 Hom.: 242 Cov.: 32

Gnomad AFR AF: 0.0685

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.0392

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0399

Gnomad FIN AF: 0.0200

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0508

Gnomad OTH AF: 0.0592

GnomAD3 exomes AF: 0.0412 AC: 10350 AN: 251142 Hom.: 266 AF XY: 0.0425 AC XY: 5773 AN XY: 135764

Gnomad AFR exome AF: 0.0699

Gnomad AMR exome AF: 0.0233

Gnomad ASJ exome AF: 0.0575

Gnomad EAS exome AF: 0.000435

Gnomad SAS exome AF: 0.0366

Gnomad FIN exome AF: 0.0231

Gnomad NFE exome AF: 0.0520

Gnomad OTH exome AF: 0.0499

GnomAD4 exome AF: 0.0466 AC: 68055 AN: 1461844 Hom.: 1809 AF XY: 0.0465 AC XY: 33815 AN XY: 727218

Gnomad4 AFR exome AF: 0.0717

Gnomad4 AMR exome AF: 0.0246

Gnomad4 ASJ exome AF: 0.0600

Gnomad4 EAS exome AF: 0.000353

Gnomad4 SAS exome AF: 0.0379

Gnomad4 FIN exome AF: 0.0237

Gnomad4 NFE exome AF: 0.0495

Gnomad4 OTH exome AF: 0.0469

GnomAD4 genome AF: 0.0518 AC: 7894 AN: 152316 Hom.: 242 Cov.: 32 AF XY: 0.0494 AC XY: 3676 AN XY: 74486

Gnomad4 AFR AF: 0.0686

Gnomad4 AMR AF: 0.0393

Gnomad4 ASJ AF: 0.0608

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0400

Gnomad4 FIN AF: 0.0200

Gnomad4 NFE AF: 0.0508

Gnomad4 OTH AF: 0.0591

Alfa AF: 0.0267 Hom.: 22

Bravo AF: 0.0541

EpiCase AF: 0.0535

EpiControl AF: 0.0552

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

EVA1A-related disorder Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Sep 13, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs148155576; hg19: chr2-75720568;