rs17011455

chr2-75563363-T-C

Variant summary

Our verdict is Benign. Variant got -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

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 -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/exons	MANE	UniProt
EVA1A	NM_032181.3	c.-192+6113A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EVA1A	ENST00000233712.5	c.-192+6113A>G		intron_variant		2		P1
EVA1A	ENST00000486696.1	n.223+6113A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0953

Gnomad4 AMR AF: 0.0261

Gnomad4 ASJ AF: 0.0285

Gnomad4 EAS AF: 0.0818

Gnomad4 SAS AF: 0.0455

Gnomad4 FIN AF: 0.0112

Gnomad4 NFE AF: 0.0273

Gnomad4 OTH AF: 0.0408

Alfa AF: 0.0392 Hom.: 56

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17011455; hg19: chr2-75790489;