chr2-75563363-T-C

Variant names:

• chr2-75563363-T-C
• rs17011455
• NM_032181.3:c.-192+6113A>G

Variant summary

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

The NM_032181.3(EVA1A):​c.-192+6113A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0472 in 152,232 control chromosomes in the GnomAD database, including 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 0.047 (256 hom., cov: 32)
• Consequence: EVA1A NM_032181.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EVA1A	NM_032181.3	c.-192+6113A>G		intron_variant	Intron 1 of 3		NP_115557.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EVA1A	ENST00000233712.5	c.-192+6113A>G		intron_variant	Intron 1 of 3	2		ENSP00000233712.1
EVA1A	ENST00000486696.1	n.223+6113A>G		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0472 AC: 7181 AN: 152114 Hom.: 255 Cov.: 32

Gnomad AFR AF: 0.0952

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0262

Gnomad ASJ AF: 0.0285

Gnomad EAS AF: 0.0814

Gnomad SAS AF: 0.0459

Gnomad FIN AF: 0.0112

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0273

Gnomad OTH AF: 0.0422

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

GnomAD4 genome AF: 0.0472 AC: 7192 AN: 152232 Hom.: 256 Cov.: 32 AF XY: 0.0463 AC XY: 3444 AN XY: 74422

African (AFR) AF: 0.0953 AC: 3958 AN: 41526

American (AMR) AF: 0.0261 AC: 399 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0285 AC: 99 AN: 3472

East Asian (EAS) AF: 0.0818 AC: 424 AN: 5182

South Asian (SAS) AF: 0.0455 AC: 219 AN: 4814

European-Finnish (FIN) AF: 0.0112 AC: 119 AN: 10612

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0273 AC: 1856 AN: 68020

Other (OTH) AF: 0.0408 AC: 86 AN: 2106

Alfa AF: 0.0387 Hom.: 289

Bravo AF: 0.0494

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.6
DANN	Benign	0.70
PhyloP100		0.26
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs17011455; hg19: chr2-75790489;