11-1988847-T-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NR_024471.1(MRPL23-AS1):n.95+979A>C 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 0.00616 in 145,502 control chromosomes in the GnomAD database, including 15 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 0.0062 ( 15 hom., cov: 21)
Consequence
MRPL23-AS1
NR_024471.1 intron, non_coding_transcript
NR_024471.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.44
Genes affected
MRPL23-AS1 (HGNC:42812): (MRPL23 antisense RNA 1)
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00616 (897/145502) while in subpopulation AFR AF= 0.021 (849/40400). AF 95% confidence interval is 0.0198. There are 15 homozygotes in gnomad4. There are 424 alleles in male gnomad4 subpopulation. Median coverage is 21. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 14 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRPL23-AS1 | NR_024471.1 | n.95+979A>C | intron_variant, non_coding_transcript_variant | ||||
MRPL23 | NM_001400176.1 | c.497+16089T>G | intron_variant | ||||
MRPL23 | XM_011520273.2 | c.497+16089T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPL23-AS1 | ENST00000419080.3 | n.168+979A>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00612 AC: 889AN: 145380Hom.: 14 Cov.: 21
GnomAD3 genomes
?
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889
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145380
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21
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00616 AC: 897AN: 145502Hom.: 15 Cov.: 21 AF XY: 0.00599 AC XY: 424AN XY: 70728
GnomAD4 genome
?
AF:
AC:
897
AN:
145502
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21
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424
AN XY:
70728
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Asia WGS
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595
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3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at