chr1-92711321-T-A

Variant names:

• chr1-92711321-T-A
• rs6680578
• NM_001350197.2:c.150-6577A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001350197.2(EVI5):​c.150-6577A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,032 control chromosomes in the GnomAD database, including 27,082 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 0.58 (27082 hom., cov: 31)
• Consequence: EVI5 NM_001350197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EVI5	NM_001350197.2	c.150-6577A>T		intron_variant	Intron 2 of 19	ENST00000684568.2	NP_001337126.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EVI5	ENST00000684568.2	c.150-6577A>T		intron_variant	Intron 2 of 19		NM_001350197.2	ENSP00000506999.1

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87813 AN: 151914 Hom.: 27082 Cov.: 31

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.578 AC: 87824 AN: 152032 Hom.: 27082 Cov.: 31 AF XY: 0.583 AC XY: 43338 AN XY: 74308

African (AFR) AF: 0.367 AC: 15219 AN: 41424

American (AMR) AF: 0.640 AC: 9781 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2378 AN: 3470

East Asian (EAS) AF: 0.917 AC: 4744 AN: 5172

South Asian (SAS) AF: 0.786 AC: 3788 AN: 4820

European-Finnish (FIN) AF: 0.629 AC: 6645 AN: 10568

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43222 AN: 67982

Other (OTH) AF: 0.565 AC: 1195 AN: 2114

Alfa AF: 0.606 Hom.: 3617

Bravo AF: 0.570

Asia WGS AF: 0.787 AC: 2736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	10
DANN	Benign	0.87
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6680578; hg19: chr1-93176878;