rs7258746

Variant names:

• chr19-53051066-A-G
• rs7258746
• NM_001191055.2:c.*207A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001191055.2(ERVV-2):​c.*207A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 490,842 control chromosomes in the GnomAD database, including 38,762 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.37 (10560 hom., cov: 28)
  • Exomes 𝑓: 0.41 (28202 hom.)
• Consequence: ERVV-2 NM_001191055.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554
• Publications: 5 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

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.*207A>G		3_prime_UTR	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.*207A>G		3_prime_UTR	Exon 2 of 2	ENSP00000472919.1	B6SEH9
	ZNF702P	ENST00000816847.1		n.382+5500T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.370 AC: 55233 AN: 149462 Hom.: 10542 Cov.: 28

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.399

GnomAD4 exome AF: 0.407 AC: 138999 AN: 341282 Hom.: 28202 Cov.: 3 AF XY: 0.404 AC XY: 72287 AN XY: 178956

African (AFR) AF: 0.287 AC: 2726 AN: 9486

American (AMR) AF: 0.540 AC: 6385 AN: 11820

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 5348 AN: 10898

East Asian (EAS) AF: 0.371 AC: 8295 AN: 22382

South Asian (SAS) AF: 0.301 AC: 9416 AN: 31294

European-Finnish (FIN) AF: 0.342 AC: 7487 AN: 21900

Middle Eastern (MID) AF: 0.519 AC: 808 AN: 1558

European-Non Finnish (NFE) AF: 0.425 AC: 90042 AN: 211822

Other (OTH) AF: 0.422 AC: 8492 AN: 20122

GnomAD4 genome AF: 0.370 AC: 55277 AN: 149560 Hom.: 10560 Cov.: 28 AF XY: 0.369 AC XY: 26883 AN XY: 72816

African (AFR) AF: 0.282 AC: 11450 AN: 40642

American (AMR) AF: 0.507 AC: 7606 AN: 15016

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1576 AN: 3456

East Asian (EAS) AF: 0.308 AC: 1526 AN: 4956

South Asian (SAS) AF: 0.292 AC: 1374 AN: 4706

European-Finnish (FIN) AF: 0.318 AC: 3148 AN: 9894

Middle Eastern (MID) AF: 0.497 AC: 143 AN: 288

European-Non Finnish (NFE) AF: 0.402 AC: 27156 AN: 67616

Other (OTH) AF: 0.400 AC: 831 AN: 2078

Alfa AF: 0.391 Hom.: 3098

Bravo AF: 0.379

Asia WGS AF: 0.272 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.8
DANN	Benign	0.59
PhyloP100		-0.55
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7258746; hg19: chr19-53554319;