rs7515577

Positions:

• chr1-92543881-C-A
• chr1-92543881-C-G
• chr1-92543881-C-T

Variant summary

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

The NM_001350197.2(EVI5):​c.2166+19761G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.852 in 152,248 control chromosomes in the GnomAD database, including 55,619 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 0.85 (55619 hom., cov: 33)
• Consequence: EVI5 NM_001350197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103

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=-0.97).
• 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	Protein	UniProt
EVI5	NM_001350197.2	c.2166+19761G>T		intron_variant		ENST00000684568.2	NP_001337126.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EVI5	ENST00000684568.2	c.2166+19761G>T		intron_variant			NM_001350197.2	ENSP00000506999	P1

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129572 AN: 152130 Hom.: 55561 Cov.: 33

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.952

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.836

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

GnomAD4 genome AF: 0.852 AC: 129692 AN: 152248 Hom.: 55619 Cov.: 33 AF XY: 0.854 AC XY: 63586 AN XY: 74442

Gnomad4 AFR AF: 0.927

Gnomad4 AMR AF: 0.869

Gnomad4 ASJ AF: 0.888

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.952

Gnomad4 FIN AF: 0.766

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.839

Alfa AF: 0.809 Hom.: 52857

Bravo AF: 0.860

Asia WGS AF: 0.956 AC: 3323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs7515577; hg19: chr1-93009438;