rs17011478

Positions:

• chr2-75565017-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032181.3(EVA1A):​c.-192+4459G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0319 in 152,302 control chromosomes in the GnomAD database, including 197 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 0.032 (197 hom., cov: 33)
• 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=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EVA1A	NM_032181.3	c.-192+4459G>A		intron_variant			NP_115557.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EVA1A	ENST00000233712.5	c.-192+4459G>A		intron_variant		2		ENSP00000233712	P1
EVA1A	ENST00000486696.1	n.223+4459G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0319 AC: 4857 AN: 152182 Hom.: 196 Cov.: 33

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0950

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0624

Gnomad FIN AF: 0.0137

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0193

Gnomad OTH AF: 0.0397

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

GnomAD4 genome AF: 0.0319 AC: 4864 AN: 152302 Hom.: 197 Cov.: 33 AF XY: 0.0330 AC XY: 2461 AN XY: 74476

Gnomad4 AFR AF: 0.0166

Gnomad4 AMR AF: 0.0955

Gnomad4 ASJ AF: 0.0527

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.0622

Gnomad4 FIN AF: 0.0137

Gnomad4 NFE AF: 0.0193

Gnomad4 OTH AF: 0.0393

Alfa AF: 0.0297 Hom.: 220

Bravo AF: 0.0429

Asia WGS AF: 0.0820 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	12
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17011478; hg19: chr2-75792143;