rs675597
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NR_149022.1(LOC497256):n.362+1172T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.013 ( 410 hom., cov: 17)
Consequence
LOC497256
NR_149022.1 intron, non_coding_transcript
NR_149022.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.89
Genes affected
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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=-0.91).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0131 (1482/113284) while in subpopulation AFR AF= 0.0443 (1377/31088). AF 95% confidence interval is 0.0423. There are 410 homozygotes in gnomad4. There are 680 alleles in male gnomad4 subpopulation. Median coverage is 17. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 410 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC497256 | NR_149022.1 | n.362+1172T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000685869.1 | n.376+1168T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0131 AC: 1482AN: 113212Hom.: 411 Cov.: 17
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?
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17
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0131 AC: 1482AN: 113284Hom.: 410 Cov.: 17 AF XY: 0.0123 AC XY: 680AN XY: 55446
GnomAD4 genome
?
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1482
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113284
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17
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680
AN XY:
55446
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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