chr5-131974979-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001009185.3(ACSL6):c.991-9C>G variant causes a splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.000948 in 1,613,306 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0023 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00080 ( 8 hom. )
Consequence
ACSL6
NM_001009185.3 splice_polypyrimidine_tract, intron
NM_001009185.3 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.9907
2
Clinical Significance
Conservation
PhyloP100: 5.46
Genes affected
ACSL6 (HGNC:16496): (acyl-CoA synthetase long chain family member 6) The protein encoded by this gene catalyzes the formation of acyl-CoA from fatty acids, ATP, and CoA, using magnesium as a cofactor. The encoded protein plays a major role in fatty acid metabolism in the brain. Translocations with the ETV6 gene are causes of myelodysplastic syndrome with basophilia, acute myelogenous leukemia with eosinophilia, and acute eosinophilic leukemia. Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Apr 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
?
Variant 5-131974979-G-C is Benign according to our data. Variant chr5-131974979-G-C is described in ClinVar as [Benign]. Clinvar id is 716862.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACSL6 | NM_001009185.3 | c.991-9C>G | splice_polypyrimidine_tract_variant, intron_variant | ENST00000651883.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACSL6 | ENST00000651883.2 | c.991-9C>G | splice_polypyrimidine_tract_variant, intron_variant | NM_001009185.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00234 AC: 356AN: 152142Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00102 AC: 254AN: 249780Hom.: 2 AF XY: 0.000859 AC XY: 116AN XY: 134986
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GnomAD4 exome AF: 0.000804 AC: 1174AN: 1461046Hom.: 8 Cov.: 31 AF XY: 0.000764 AC XY: 555AN XY: 726734
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GnomAD4 genome ? AF: 0.00233 AC: 355AN: 152260Hom.: 3 Cov.: 32 AF XY: 0.00206 AC XY: 153AN XY: 74442
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 03, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Calibrated prediction
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dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at