Genetic Variant ERVV-2:p.Ser37Leu (chr19-53049361-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001191055.2(ERVV-2):c.110C>T(p.Ser37Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0031 ( 2 hom., cov: 13)

Exomes 𝑓: 0.0039 ( 11 hom. )

Consequence

ERVV-2
NM_001191055.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.487

Variant links:

Genes affected

ERVV-2 (HGNC:39051): (endogenous retrovirus group V member 2, envelope) Many different human endogenous retrovirus (HERV) families are expressed in normal placental tissue at high levels, suggesting that HERVs are functionally important in reproduction. This gene is part of an HERV provirus on human chromosome 19 that has inactivating mutations in the gag and pol genes. This envelope glycoprotein gene appears to have been selectively preserved. The gene's protein product is expressed in the placenta and acts as a syncytin in Old World monkeys, but has lost the fusogenic activity in humans and other primate lineages. [provided by RefSeq, Jun 2015]

ERVV-2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.007838368).

BP6

Variant 19-53049361-C-T is Benign according to our data. Variant chr19-53049361-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3388444.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ERVV-2	NM_001191055.2 link	c.110C>T	p.Ser37Leu	missense_variant	Exon 2 of 2	ENST00000601417.3	NP_001177984.1	B6SEH9M9QSX5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ERVV-2	ENST00000601417.3 link	c.110C>T	p.Ser37Leu	missense_variant	Exon 2 of 2	4	NM_001191055.2	ENSP00000472919.1		B6SEH9

Frequencies

GnomAD3 genomes

AF:

0.00308

AC:

320

AN:

104058

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000949

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00194

Gnomad ASJ

AF:

0.000737

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00143

Gnomad FIN

AF:

0.00813

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00430

Gnomad OTH

AF:

0.00223

GnomAD3 exomes

AF:

0.00285

AC:

223

AN:

78194

Hom.:

AF XY:

0.00279

AC XY:

114

AN XY:

40872

show subpopulations

Gnomad AFR exome

AF:

0.00107

Gnomad AMR exome

AF:

0.00233

Gnomad ASJ exome

AF:

0.00180

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000910

Gnomad FIN exome

AF:

0.00473

Gnomad NFE exome

AF:

0.00490

Gnomad OTH exome

AF:

0.00311

GnomAD4 exome

AF:

0.00387

AC:

3049

AN:

787826

Hom.:

Cov.:

AF XY:

0.00389

AC XY:

1560

AN XY:

401400

show subpopulations

Gnomad4 AFR exome

AF:

0.000888

Gnomad4 AMR exome

AF:

0.00169

Gnomad4 ASJ exome

AF:

0.00199

Gnomad4 EAS exome

AF:

0.0000303

Gnomad4 SAS exome

AF:

0.00208

Gnomad4 FIN exome

AF:

0.0135

Gnomad4 NFE exome

AF:

0.00400

Gnomad4 OTH exome

AF:

0.00422

GnomAD4 genome

AF:

0.00308

AC:

321

AN:

104146

Hom.:

Cov.:

AF XY:

0.00300

AC XY:

145

AN XY:

48412

show subpopulations

Gnomad4 AFR

AF:

0.000945

Gnomad4 AMR

AF:

0.00193

Gnomad4 ASJ

AF:

0.000737

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00179

Gnomad4 FIN

AF:

0.00813

Gnomad4 NFE

AF:

0.00430

Gnomad4 OTH

AF:

0.00219

Alfa

AF:

0.00485

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Nov 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ERVV-2: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.40

BayesDel_addAF

Benign

-0.62

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Benign

0.68

DEOGEN2

Benign

0.0045

FATHMM_MKL

Benign

0.0033

LIST_S2

Benign

0.68

M_CAP

Benign

0.036

MetaRNN

Benign

0.0078

MutationAssessor

Benign

0.69

PrimateAI

Benign

0.44

Sift4G

Pathogenic

0.0

Vest4

0.13

MVP

0.38

GERP RS

0.23

Varity_R

0.082

gMVP

0.082

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over