chr6-13604478-A-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The ENST00000379262.8(SIRT5):c.860A>T(p.His287Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0176 in 1,554,208 control chromosomes in the GnomAD database, including 327 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Consequence
ENST00000379262.8 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIRT5 | NM_012241.5 | c.857+3529A>T | intron_variant | ENST00000606117.2 | |||
LOC105374938 | XR_007059460.1 | n.2164+1953T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIRT5 | ENST00000606117.2 | c.857+3529A>T | intron_variant | 1 | NM_012241.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0147 AC: 2241AN: 152236Hom.: 28 Cov.: 33
GnomAD3 exomes AF: 0.0149 AC: 3656AN: 245126Hom.: 53 AF XY: 0.0150 AC XY: 1987AN XY: 132730
GnomAD4 exome AF: 0.0179 AC: 25094AN: 1401854Hom.: 299 Cov.: 25 AF XY: 0.0175 AC XY: 12271AN XY: 700558
GnomAD4 genome ? AF: 0.0147 AC: 2240AN: 152354Hom.: 28 Cov.: 33 AF XY: 0.0156 AC XY: 1159AN XY: 74504
ClinVar
Submissions by phenotype
not provided Other:1
not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | Variant interpretted as Likely benign and reported on 10-30-2014 by Lab or GTR ID 320384. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at