chr7-64992198-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001007253.4(ERV3-1):c.829G>A(p.Ala277Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00117 in 766,272 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0034 ( 4 hom., cov: 32)

Exomes 𝑓: 0.00061 ( 0 hom. )

Consequence

ERV3-1
NM_001007253.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.202

Publications

3 publications found

Variant links:

Genes affected

ERV3-1 (HGNC:3454): (endogenous retrovirus group 3 member 1, envelope) This gene contains sequence derived from endogenous retrovirus, and is therefore similar to multiple other loci in the genome. Transcripts at this locus encode a conserved protein with a predicted signal peptide and similarity to the Env polyprotein. This protein is overexpressed in colorectal and other cancers. [provided by RefSeq, Jan 2017]

ERV3-1 links:

ZNF117 (HGNC:12897): (zinc finger protein 117) This gene encodes a protein containing multiple C2H2-type zinc finger motifs. Readthrough transcription occurs between this gene and the upstream endogenous retrovirus group 3 member 1 (ERV3-1) locus, and may result in additional transcript variants encoding the zinc finger protein. [provided by RefSeq, Jan 2017]

ZNF117 links:

ERV3-1-ZNF117 (HGNC:):

ERV3-1-ZNF117 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00222376).

BP6

Variant 7-64992198-C-T is Benign according to our data. Variant chr7-64992198-C-T is described in ClinVar as Benign. ClinVar VariationId is 709122.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001007253.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ERV3-1	NM_001007253.4	MANE Select	c.829G>A	p.Ala277Thr	missense	Exon 2 of 2	NP_001007254.2	Q14264
ERV3-1	NM_001396062.1		c.829G>A	p.Ala277Thr	missense	Exon 2 of 2	NP_001382991.1	Q14264
ERV3-1-ZNF117	NM_001348050.2		c.-195-10082G>A		intron	N/A	NP_001334979.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ERV3-1	ENST00000394323.3	TSL:2 MANE Select	c.829G>A	p.Ala277Thr	missense	Exon 2 of 2	ENSP00000391594.1	Q14264
ZNF117	ENST00000714027.1		c.-2447G>A		5_prime_UTR	Exon 2 of 5	ENSP00000519317.1	Q03924
ZNF117	ENST00000714026.1		c.-195-10082G>A		intron	N/A	ENSP00000519316.1	Q03924

Frequencies

GnomAD3 genomes

AF:

0.00343

AC:

521

AN:

152016

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0121

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000393

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000588

Gnomad OTH

AF:

0.000957

GnomAD2 exomes

AF:

0.000841

AC:

197

AN:

234322

AF XY:

0.000578

show subpopulations

Gnomad AFR exome

AF:

0.0114

Gnomad AMR exome

AF:

0.000203

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000395

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000551

Gnomad OTH exome

AF:

0.000677

GnomAD4 exome

AF:

0.000606

AC:

372

AN:

614138

Hom.:

Cov.:

AF XY:

0.000486

AC XY:

163

AN XY:

335610

show subpopulations

African (AFR)

AF:

0.0105

AC:

186

AN:

17690

American (AMR)

AF:

0.000252

AC:

AN:

43734

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

20984

East Asian (EAS)

AF:

0.00347

AC:

125

AN:

36066

South Asian (SAS)

AF:

0.0000143

AC:

AN:

69798

European-Finnish (FIN)

AF:

0.00

AC:

AN:

38846

Middle Eastern (MID)

AF:

0.000482

AC:

AN:

4146

European-Non Finnish (NFE)

AF:

0.0000686

AC:

AN:

349884

Other (OTH)

AF:

0.000697

AC:

AN:

32990

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

118

147

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00343

AC:

522

AN:

152134

Hom.:

Cov.:

AF XY:

0.00321

AC XY:

239

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.0121

AC:

502

AN:

41488

American (AMR)

AF:

0.000393

AC:

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3464

East Asian (EAS)

AF:

0.00155

AC:

AN:

5172

South Asian (SAS)

AF:

0.00

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10586

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0000588

AC:

AN:

67998

Other (OTH)

AF:

0.000947

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

113

141

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000798

Hom.:

Bravo

AF:

0.00367

ESP6500AA

AF:

0.0121

AC:

ESP6500EA

AF:

0.000243

AC:

ExAC

AF:

0.00107

AC:

127

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.000218

EpiControl

AF:

0.0000593

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.098

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.78

CADD

Benign

9.7

(source)

DANN

Benign

0.97

DEOGEN2

Benign

0.0015

Eigen

Benign

-0.99

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.0072

LIST_S2

Benign

0.40

MetaRNN

Benign

0.0022

MetaSVM

Benign

-0.97

MutationAssessor

Benign

0.0

PhyloP100

0.20

PrimateAI

Benign

0.48

PROVEAN

Benign

0.060

REVEL

Benign

0.015

Sift

Benign

0.050

Sift4G

Benign

0.30

Polyphen

0.10

Vest4

0.14

MVP

0.085

MPC

0.078

ClinPred

0.021

GERP RS

0.11

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.050

gMVP

0.20

Mutation Taster

=99/1

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over