1-92573954-T-C

Position:

• chr1-92573954-T-C

Variant summary

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

The NM_001350197.2(EVI5):​c.2071-10217A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 152,122 control chromosomes in the GnomAD database, including 64,638 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 0.92 (64638 hom., cov: 31)
• Consequence: EVI5 NM_001350197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

EVI5 (HGNC:3501): (ecotropic viral integration site 5) Enables GTPase activator activity and small GTPase binding activity. Involved in positive regulation of GTPase activity and retrograde transport, endosome to Golgi. Located in cytosol. [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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EVI5	NM_001350197.2	c.2071-10217A>G		intron_variant		ENST00000684568.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EVI5	ENST00000684568.2	c.2071-10217A>G		intron_variant			NM_001350197.2	P1

Frequencies

GnomAD3 genomes AF: 0.921 AC: 140023 AN: 152004 Hom.: 64587 Cov.: 31

Gnomad AFR AF: 0.946

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.959

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.921 AC: 140134 AN: 152122 Hom.: 64638 Cov.: 31 AF XY: 0.922 AC XY: 68593 AN XY: 74358

Gnomad4 AFR AF: 0.946

Gnomad4 AMR AF: 0.934

Gnomad4 ASJ AF: 0.959

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.967

Gnomad4 FIN AF: 0.884

Gnomad4 NFE AF: 0.900

Gnomad4 OTH AF: 0.912

Alfa AF: 0.914 Hom.: 10265

Bravo AF: 0.924

Asia WGS AF: 0.964 AC: 3350 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.53

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

Publications

LitVar

Other links and lift over

dbSNP: rs2391164; hg19: chr1-93039511;