19-49858944-T-G

Variant names:

• chr19-49858944-T-G
• rs7257463
• NM_001394010.1:c.1041+291T>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001394010.1(PTOV1):​c.1041+291T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PTOV1 NM_001394010.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46
• Publications: 6 publications found

Genes affected

PTOV1 (HGNC:9632): (PTOV1 extended AT-hook containing adaptor protein) This gene encodes a protein that was found to be overexpressed in prostate adenocarcinomas. The encoded protein was found to interact with the lipid raft protein flotillin-1 and shuttle it from the cytoplasm to the nucleus in a cell cycle dependent manner. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Feb 2015]

PTOV1-AS2 (HGNC:51284): (PTOV1 antisense RNA 2)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTOV1	NM_001394010.1	c.1041+291T>G		intron_variant	Intron 10 of 11	ENST00000391842.6	NP_001380939.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTOV1	ENST00000391842.6	c.1041+291T>G		intron_variant	Intron 10 of 11	5	NM_001394010.1	ENSP00000375717.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 154388 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 79032

African (AFR) AF: 0.00 AC: 0 AN: 5716

American (AMR) AF: 0.00 AC: 0 AN: 6546

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5888

East Asian (EAS) AF: 0.00 AC: 0 AN: 13634

South Asian (SAS) AF: 0.00 AC: 0 AN: 6530

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9720

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 788

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 95626

Other (OTH) AF: 0.00 AC: 0 AN: 9940

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 1176

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.39
DANN	Benign	0.70
PhyloP100		-2.5

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: rs7257463; hg19: chr19-50362201;