chr19-53049361-C-T
Variant names:
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
NM_001191055.2 missense
Scores
1
1
10
Clinical Significance
Conservation
PhyloP100: 0.487
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]
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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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00308 AC: 320AN: 104058Hom.: 2 Cov.: 13
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GnomAD3 exomes AF: 0.00285 AC: 223AN: 78194Hom.: 0 AF XY: 0.00279 AC XY: 114AN XY: 40872
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GnomAD4 exome AF: 0.00387 AC: 3049AN: 787826Hom.: 11 Cov.: 11 AF XY: 0.00389 AC XY: 1560AN XY: 401400
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GnomAD4 genome AF: 0.00308 AC: 321AN: 104146Hom.: 2 Cov.: 13 AF XY: 0.00300 AC XY: 145AN XY: 48412
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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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Benign
T
MutationAssessor
Benign
N
PrimateAI
Benign
T
Sift4G
Pathogenic
D
Vest4
MVP
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at