2-75493442-CGCTGTCGCT-C

Variant names:

• chr2-75493442-CGCTGTCGCT-C
• rs148155576
• NM_001135032.2:c.244_252delAGCGACAGC

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP6 BA1

The NM_001135032.2(EVA1A):​c.244_252delAGCGACAGC​(p.Ser82_Ser84del) variant causes a conservative 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 (no stars).

• Frequency:
  • Genomes: 𝑓 0.052 (242 hom., cov: 32)
  • Exomes 𝑓: 0.047 (1809 hom.)
• Consequence: EVA1A NM_001135032.2 conservative_inframe_deletion
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: 5.05
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -9 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 VariationId is 3055669.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0665 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001135032.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EVA1A	NM_001135032.2	MANE Select	c.244_252delAGCGACAGC	p.Ser82_Ser84del	conservative_inframe_deletion	Exon 4 of 4	NP_001128504.1	Q9H8M9
	EVA1A	NM_001369524.1		c.244_252delAGCGACAGC	p.Ser82_Ser84del	conservative_inframe_deletion	Exon 6 of 6	NP_001356453.1	Q9H8M9
	EVA1A	NM_001369525.1		c.244_252delAGCGACAGC	p.Ser82_Ser84del	conservative_inframe_deletion	Exon 5 of 5	NP_001356454.1	Q9H8M9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EVA1A	ENST00000393913.8	TSL:1 MANE Select	c.244_252delAGCGACAGC	p.Ser82_Ser84del	conservative_inframe_deletion	Exon 4 of 4	ENSP00000377490.3	Q9H8M9
	EVA1A	ENST00000910300.1		c.301_309delAGCGACAGC	p.Ser101_Ser103del	conservative_inframe_deletion	Exon 4 of 4	ENSP00000580359.1
	EVA1A	ENST00000910305.1		c.301_309delAGCGACAGC	p.Ser101_Ser103del	conservative_inframe_deletion	Exon 3 of 3	ENSP00000580364.1

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

GnomAD2 exomes AF: 0.0412 AC: 10350 AN: 251142 AF XY: 0.0425

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 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

African (AFR) AF: 0.0717 AC: 2399 AN: 33476

American (AMR) AF: 0.0246 AC: 1099 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.0600 AC: 1568 AN: 26136

East Asian (EAS) AF: 0.000353 AC: 14 AN: 39700

South Asian (SAS) AF: 0.0379 AC: 3267 AN: 86254

European-Finnish (FIN) AF: 0.0237 AC: 1266 AN: 53406

Middle Eastern (MID) AF: 0.0983 AC: 567 AN: 5766

European-Non Finnish (NFE) AF: 0.0495 AC: 55044 AN: 1111990

Other (OTH) AF: 0.0469 AC: 2831 AN: 60392

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

African (AFR) AF: 0.0686 AC: 2851 AN: 41560

American (AMR) AF: 0.0393 AC: 601 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0608 AC: 211 AN: 3468

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5180

South Asian (SAS) AF: 0.0400 AC: 193 AN: 4828

European-Finnish (FIN) AF: 0.0200 AC: 212 AN: 10626

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0508 AC: 3457 AN: 68024

Other (OTH) AF: 0.0591 AC: 125 AN: 2116

Alfa AF: 0.0267 Hom.: 22

Bravo AF: 0.0541

EpiCase AF: 0.0535

EpiControl AF: 0.0552

ClinVar

ClinVar submissions

Significance: Benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	EVA1A-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.1
Mutation Taster		=183/17	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs148155576; hg19: chr2-75720568; COSMIC: COSV52056430; COSMIC: COSV52056430;