rs10491648
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_018465.4(PLGRKT):c.81+19030T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00351 in 152,324 control chromosomes in the GnomAD database, including 2 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 0.0035 ( 2 hom., cov: 32)
Consequence
PLGRKT
NM_018465.4 intron
NM_018465.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0290
Genes affected
PLGRKT (HGNC:23633): (plasminogen receptor with a C-terminal lysine) Predicted to be involved in positive regulation of plasminogen activation. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BS2
?
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLGRKT | NM_018465.4 | c.81+19030T>C | intron_variant | ENST00000223864.7 | |||
PLGRKT | XM_005251510.6 | c.81+19030T>C | intron_variant | ||||
PLGRKT | XM_011517960.3 | c.81+19030T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLGRKT | ENST00000223864.7 | c.81+19030T>C | intron_variant | 1 | NM_018465.4 | P1 | |||
PLGRKT | ENST00000472145.5 | n.288+19030T>C | intron_variant, non_coding_transcript_variant | 2 | |||||
PLGRKT | ENST00000473877.1 | n.213+19030T>C | intron_variant, non_coding_transcript_variant | 3 | |||||
PLGRKT | ENST00000482696.5 | n.292+19030T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00351 AC: 534AN: 152206Hom.: 2 Cov.: 32
GnomAD3 genomes
?
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534
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00351 AC: 535AN: 152324Hom.: 2 Cov.: 32 AF XY: 0.00365 AC XY: 272AN XY: 74490
GnomAD4 genome
?
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535
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152324
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32
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272
AN XY:
74490
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6
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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