rs542274378
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001191055.2(ERVV-2):c.952C>A(p.Gln318Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 11/16 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000040 ( 0 hom., cov: 22)
Exomes 𝑓: 0.0000096 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ERVV-2
NM_001191055.2 missense
NM_001191055.2 missense
Scores
12
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.305
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 Likely_benign. Variant got -2 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.09717655).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000403 AC: 6AN: 148708Hom.: 0 Cov.: 22
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GnomAD3 exomes AF: 0.00000954 AC: 1AN: 104784Hom.: 0 AF XY: 0.0000176 AC XY: 1AN XY: 56736
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000964 AC: 10AN: 1036858Hom.: 0 Cov.: 15 AF XY: 0.0000134 AC XY: 7AN XY: 523574
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000403 AC: 6AN: 148708Hom.: 0 Cov.: 22 AF XY: 0.0000276 AC XY: 2AN XY: 72384
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
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
T
MetaRNN
Benign
T
MutationAssessor
Benign
L
PrimateAI
Benign
T
Sift4G
Benign
T
Vest4
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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