rs10517138
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The XR_001741640.2(LOC105374557):n.830+10658G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00565 in 152,186 control chromosomes in the GnomAD database, including 6 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 0.0057 ( 6 hom., cov: 32)
Consequence
LOC105374557
XR_001741640.2 intron, non_coding_transcript
XR_001741640.2 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0230
Genes affected
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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=-0.79).
BS2
?
High Homozygotes in GnomAd4 at 6 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC105374557 | XR_001741640.2 | n.830+10658G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.00564 AC: 858AN: 152068Hom.: 6 Cov.: 32
GnomAD3 genomes
?
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858
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152068
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Cov.:
32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00565 AC: 860AN: 152186Hom.: 6 Cov.: 32 AF XY: 0.00595 AC XY: 443AN XY: 74414
GnomAD4 genome
?
AF:
AC:
860
AN:
152186
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Cov.:
32
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443
AN XY:
74414
Gnomad4 AFR
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at