rs10747448

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001350197.2(EVI5):​c.1392+6946A>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 152,204 control chromosomes in the GnomAD database, including 64,667 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 ( 64667 hom., cov: 32)

Consequence

EVI5
NM_001350197.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.212
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
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
EVI5NM_001350197.2 linkuse as main transcriptc.1392+6946A>G intron_variant ENST00000684568.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
EVI5ENST00000684568.2 linkuse as main transcriptc.1392+6946A>G intron_variant NM_001350197.2 P1

Frequencies

GnomAD3 genomes
AF:
0.921
AC:
140102
AN:
152086
Hom.:
64616
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.945
Gnomad AMI
AF:
0.955
Gnomad AMR
AF:
0.934
Gnomad ASJ
AF:
0.959
Gnomad EAS
AF:
0.968
Gnomad SAS
AF:
0.967
Gnomad FIN
AF:
0.885
Gnomad MID
AF:
0.937
Gnomad NFE
AF:
0.900
Gnomad OTH
AF:
0.913
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.921
AC:
140213
AN:
152204
Hom.:
64667
Cov.:
32
AF XY:
0.922
AC XY:
68632
AN XY:
74406
show subpopulations
Gnomad4 AFR
AF:
0.945
Gnomad4 AMR
AF:
0.934
Gnomad4 ASJ
AF:
0.959
Gnomad4 EAS
AF:
0.968
Gnomad4 SAS
AF:
0.967
Gnomad4 FIN
AF:
0.885
Gnomad4 NFE
AF:
0.900
Gnomad4 OTH
AF:
0.913
Alfa
AF:
0.915
Hom.:
10771
Bravo
AF:
0.924
Asia WGS
AF:
0.962
AC:
3348
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
4.0
DANN
Benign
0.44

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10747448; hg19: chr1-93121330; API