rs17342441
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000426018.1(MTND5P26):n.920A>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.078 in 110,786 control chromosomes in the GnomAD database, including 315 homozygotes. There are 2,572 hemizygotes in GnomAD. 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 0.078 ( 315 hom., 2572 hem., cov: 22)
Failed GnomAD Quality Control
Consequence
MTND5P26
ENST00000426018.1 non_coding_transcript_exon
ENST00000426018.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.97
Genes affected
MTND5P26 (HGNC:42295): (MT-ND5 pseudogene 26)
LINC00630 (HGNC:44263): (long intergenic non-protein coding RNA 630)
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARMCX5-GPRASP2 | NR_146584.3 | n.1219-20687A>C | intron_variant, non_coding_transcript_variant | ||||
LINC00630 | NR_146589.1 | n.190-21663A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTND5P26 | ENST00000426018.1 | n.920A>C | non_coding_transcript_exon_variant | 2/2 | |||||
LINC00630 | ENST00000440496.5 | n.233-11686A>C | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0780 AC: 8634AN: 110737Hom.: 315 Cov.: 22 AF XY: 0.0774 AC XY: 2570AN XY: 33207
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
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GnomAD4 genome ? AF: 0.0780 AC: 8636AN: 110786Hom.: 315 Cov.: 22 AF XY: 0.0773 AC XY: 2572AN XY: 33266
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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