rs1264440
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001025091.2(ABCF1):c.916-99A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 1,276,494 control chromosomes in the GnomAD database, including 305,328 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 0.69 ( 36513 hom., cov: 31)
Exomes 𝑓: 0.69 ( 268815 hom. )
Consequence
ABCF1
NM_001025091.2 intron
NM_001025091.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.18
Genes affected
ABCF1 (HGNC:70): (ATP binding cassette subfamily F member 1) The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the GCN20 subfamily. Unlike other members of the superfamily, this protein lacks the transmembrane domains which are characteristic of most ABC transporters. This protein may be regulated by tumor necrosis factor-alpha and play a role in enhancement of protein synthesis and the inflammation process. [provided by RefSeq, Jul 2008]
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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=-0.71).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCF1 | NM_001025091.2 | c.916-99A>G | intron_variant | ENST00000326195.13 | |||
ABCF1 | NM_001090.3 | c.802-99A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCF1 | ENST00000326195.13 | c.916-99A>G | intron_variant | 1 | NM_001025091.2 | A1 | |||
ABCF1 | ENST00000376545.7 | c.802-99A>G | intron_variant | 1 | |||||
ABCF1 | ENST00000475993.1 | c.167-99A>G | intron_variant, NMD_transcript_variant | 1 | |||||
ABCF1 | ENST00000441867.6 | c.919-99A>G | intron_variant | 5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.692 AC: 105043AN: 151852Hom.: 36478 Cov.: 31
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GnomAD4 exome AF: 0.689 AC: 774250AN: 1124524Hom.: 268815 AF XY: 0.695 AC XY: 395207AN XY: 568752
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GnomAD4 genome ? AF: 0.692 AC: 105131AN: 151970Hom.: 36513 Cov.: 31 AF XY: 0.691 AC XY: 51359AN XY: 74274
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at