rs4970700

Positions:

• chr1-92509936-A-G

Variant summary

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

The NM_001350197.2(EVI5):​c.*3720T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,070 control chromosomes in the GnomAD database, including 42,710 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 0.74 (42710 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: EVI5 NM_001350197.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EVI5	NM_001350197.2	c.*3720T>C		3_prime_UTR_variant	20/20	ENST00000684568.2	NP_001337126.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EVI5	ENST00000684568	c.*3720T>C		3_prime_UTR_variant	20/20		NM_001350197.2	ENSP00000506999.1

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112270 AN: 151952 Hom.: 42666 Cov.: 31

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.687

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.739 AC: 112374 AN: 152070 Hom.: 42710 Cov.: 31 AF XY: 0.740 AC XY: 55024 AN XY: 74318

Gnomad4 AFR AF: 0.898

Gnomad4 AMR AF: 0.715

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.944

Gnomad4 SAS AF: 0.849

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.691

Alfa AF: 0.692 Hom.: 12062

Bravo AF: 0.751

Asia WGS AF: 0.886 AC: 3080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.50

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: rs4970700; hg19: chr1-92975493;