rs10782922

chr1-92509038-G-Achr1-92509038-G-Cchr1-92509038-G-T

Variant summary

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

The NM_001350197.2(EVI5):c.*4618C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.852 in 152,210 control chromosomes in the GnomAD database, including 55,693 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 (55691 hom., cov: 32)
  • Exomes 𝑓: 0.57 (2 hom.)
• Consequence: EVI5 NM_001350197.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.609

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=-0.9).
• 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.*4618C>T		3_prime_UTR_variant	20/20	ENST00000684568.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EVI5	ENST00000684568.2	c.*4618C>T		3_prime_UTR_variant	20/20		NM_001350197.2	P1

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129625 AN: 152078 Hom.: 55632 Cov.: 32

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.836

GnomAD4 exome AF: 0.571 AC: 8 AN: 14 Hom.: 2 Cov.: 0 AF XY: 0.600 AC XY: 6 AN XY: 10

Gnomad4 FIN exome AF: 0.583

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.852 AC: 129746 AN: 152196 Hom.: 55691 Cov.: 32 AF XY: 0.855 AC XY: 63620 AN XY: 74416

Gnomad4 AFR AF: 0.929

Gnomad4 AMR AF: 0.869

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.952

Gnomad4 FIN AF: 0.767

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.838

Alfa AF: 0.814 Hom.: 49838

Bravo AF: 0.860

Asia WGS AF: 0.956 AC: 3301 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.9
Dann	Benign	0.56

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: rs10782922; hg19: chr1-92974595;