2-75518123-G-A

Variant names:

• chr2-75518123-G-A
• rs781234792
• NM_001135032.2:c.18C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001135032.2(EVA1A):​c.18C>T​(p.Ser6Ser) variant causes a synonymous change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: EVA1A NM_001135032.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.15
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

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.18C>T	p.Ser6Ser	synonymous	Exon 3 of 4	NP_001128504.1	Q9H8M9
	EVA1A	NM_001369524.1		c.18C>T	p.Ser6Ser	synonymous	Exon 5 of 6	NP_001356453.1	Q9H8M9
	EVA1A	NM_001369525.1		c.18C>T	p.Ser6Ser	synonymous	Exon 4 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.18C>T	p.Ser6Ser	synonymous	Exon 3 of 4	ENSP00000377490.3	Q9H8M9
	EVA1A	ENST00000910300.1		c.18C>T	p.Ser6Ser	synonymous	Exon 2 of 4	ENSP00000580359.1
	EVA1A	ENST00000910305.1		c.18C>T	p.Ser6Ser	synonymous	Exon 1 of 3	ENSP00000580364.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.5
DANN	Benign	0.66
PhyloP100		5.1
PromoterAI		-0.036	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs781234792; hg19: chr2-75745249;