rs551356870

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

1
1
10

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]

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-2NM_001191055.2 linkc.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-2ENST00000601417.3 linkc.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.:
2
Cov.:
13
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.:
0
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.:
11
Cov.:
11
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.:
2
Cov.:
13
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.:
1

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
T
BayesDel_noAF
Benign
-0.66
CADD
Benign
20
DANN
Benign
0.68
DEOGEN2
Benign
0.0045
T
FATHMM_MKL
Benign
0.0033
N
LIST_S2
Benign
0.68
T
M_CAP
Benign
0.036
D
MetaRNN
Benign
0.0078
T
MutationAssessor
Benign
0.69
N
PrimateAI
Benign
0.44
T
Sift4G
Pathogenic
0.0
D
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.

Other links and lift over

dbSNP: rs551356870; hg19: chr19-53552614; API