chr1-92754350-C-T

Variant names:

• chr1-92754350-C-T
• rs6604015
• NM_001350197.2:c.-81-17723G>A

Variant summary

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

The NM_001350197.2(EVI5):​c.-81-17723G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.919 in 152,272 control chromosomes in the GnomAD database, including 64,406 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 (64406 hom., cov: 32)
• Consequence: EVI5 NM_001350197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 11 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001350197.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EVI5	NM_001350197.2	MANE Select	c.-81-17723G>A		intron	N/A	NP_001337126.1
	EVI5	NM_001308248.2		c.52-17723G>A		intron	N/A	NP_001295177.1
	EVI5	NM_001377210.1		c.43-17723G>A		intron	N/A	NP_001364139.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EVI5	ENST00000684568.2	MANE Select	c.-81-17723G>A		intron	N/A	ENSP00000506999.1
	EVI5	ENST00000540033.3	TSL:1	c.52-17723G>A		intron	N/A	ENSP00000440826.2
	EVI5	ENST00000370331.5	TSL:1	c.52-17723G>A		intron	N/A	ENSP00000359356.1

Frequencies

GnomAD3 genomes AF: 0.919 AC: 139852 AN: 152154 Hom.: 64355 Cov.: 32

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.919 AC: 139963 AN: 152272 Hom.: 64406 Cov.: 32 AF XY: 0.920 AC XY: 68510 AN XY: 74442

African (AFR) AF: 0.937 AC: 38952 AN: 41562

American (AMR) AF: 0.933 AC: 14273 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3336 AN: 3472

East Asian (EAS) AF: 0.969 AC: 5030 AN: 5192

South Asian (SAS) AF: 0.967 AC: 4670 AN: 4830

European-Finnish (FIN) AF: 0.883 AC: 9358 AN: 10592

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.901 AC: 61277 AN: 68016

Other (OTH) AF: 0.912 AC: 1924 AN: 2110

Alfa AF: 0.915 Hom.: 11079

Bravo AF: 0.921

Asia WGS AF: 0.963 AC: 3349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.44
PhyloP100		-0.23
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: rs6604015; hg19: chr1-93219907;