chr1-92509936-A-G

Variant names:

• chr1-92509936-A-G
• rs4970700
• NM_001350197.2:c.*3720T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 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.*3720T>C		3_prime_UTR	Exon 20 of 20	NP_001337126.1
	EVI5	NM_001308248.2		c.*3720T>C		3_prime_UTR	Exon 19 of 19	NP_001295177.1
	EVI5	NM_001377210.1		c.*3720T>C		3_prime_UTR	Exon 19 of 19	NP_001364139.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EVI5	ENST00000684568.2	MANE Select	c.*3720T>C		3_prime_UTR	Exon 20 of 20	ENSP00000506999.1
	EVI5	ENST00000370331.5	TSL:1	c.*3720T>C		3_prime_UTR	Exon 18 of 18	ENSP00000359356.1
	EVI5	ENST00000706845.1		n.*6034T>C		non_coding_transcript_exon	Exon 22 of 22	ENSP00000516587.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.898 AC: 37271 AN: 41496

American (AMR) AF: 0.715 AC: 10913 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2376 AN: 3468

East Asian (EAS) AF: 0.944 AC: 4890 AN: 5178

South Asian (SAS) AF: 0.849 AC: 4094 AN: 4822

European-Finnish (FIN) AF: 0.627 AC: 6607 AN: 10532

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43872 AN: 67992

Other (OTH) AF: 0.691 AC: 1456 AN: 2108

Alfa AF: 0.699 Hom.: 13671

Bravo AF: 0.751

Asia WGS AF: 0.886 AC: 3080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.50
PhyloP100		-0.015
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: rs4970700; hg19: chr1-92975493;