NM_001191055.2:c.83T>C

Variant names:

• chr19-53049334-T-C
• rs938056857
• NM_001191055.2:c.83T>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001191055.2(ERVV-2):​c.83T>C​(p.Leu28Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L28I) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 15)
  • Exomes 𝑓: 0.0000011 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ERVV-2 NM_001191055.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.492
• Publications: 0 publications found

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]

ZNF702P (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001191055.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERVV-2	NM_001191055.2	MANE Select	c.83T>C	p.Leu28Pro	missense	Exon 2 of 2	NP_001177984.1	B6SEH9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERVV-2	ENST00000601417.3	TSL:4 MANE Select	c.83T>C	p.Leu28Pro	missense	Exon 2 of 2	ENSP00000472919.1	B6SEH9
	ZNF702P	ENST00000816847.1		n.383-6770A>G		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 15

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000110 AC: 1 AN: 907182 Hom.: 0 Cov.: 13 AF XY: 0.00 AC XY: 0 AN XY: 457158

African (AFR) AF: 0.0000472 AC: 1 AN: 21182

American (AMR) AF: 0.00 AC: 0 AN: 24896

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18946

East Asian (EAS) AF: 0.00 AC: 0 AN: 33596

South Asian (SAS) AF: 0.00 AC: 0 AN: 61110

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31876

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3880

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 670196

Other (OTH) AF: 0.00 AC: 0 AN: 41500

GnomAD4 genome Cov.: 15

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.67
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.54
CADD	Benign	18
DANN	Benign	0.63
DEOGEN2	Benign	0.0031	T
FATHMM_MKL	Benign	0.0032	N
LIST_S2	Benign	0.44	T
M_CAP	Benign	0.014	T
MetaRNN	Uncertain	0.55	D
MutationAssessor	Benign	0.20	N
PhyloP100		0.49
PrimateAI	Benign	0.43	T
Sift4G	Pathogenic	0.0	D
Vest4		0.67
MVP		0.43
GERP RS		0.23
Varity_R		0.46
gMVP		0.26
Mutation Taster		=91/9	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs938056857; hg19: chr19-53552587;