rs10247016
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001142928.2(LRRC61):c.-145+3070C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000723 in 152,120 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000072 ( 0 hom., cov: 33)
Consequence
LRRC61
NM_001142928.2 intron
NM_001142928.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.337
Genes affected
LRRC61 (HGNC:21704): (leucine rich repeat containing 61) Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC61 | NM_001142928.2 | c.-145+3070C>A | intron_variant | ENST00000359623.9 | |||
LRRC61 | NM_001363433.1 | c.-145+3070C>A | intron_variant | ||||
LRRC61 | NM_001363434.1 | c.-145+3070C>A | intron_variant | ||||
LRRC61 | NM_023942.3 | c.-145+5520C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC61 | ENST00000359623.9 | c.-145+3070C>A | intron_variant | 2 | NM_001142928.2 | P1 | |||
LRRC61 | ENST00000323078.7 | c.-145+5520C>A | intron_variant | 1 | P1 | ||||
ENST00000343855.6 | n.1190C>A | non_coding_transcript_exon_variant | 3/3 | ||||||
LRRC61 | ENST00000493307.1 | c.-145+3070C>A | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000724 AC: 11AN: 152002Hom.: 0 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152120Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74364
GnomAD4 genome
?
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Calibrated prediction
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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