chr6-30584276-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001025091.2(ABCF1):c.1187G>A(p.Arg396Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000916 in 1,613,058 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001025091.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCF1 | NM_001025091.2 | c.1187G>A | p.Arg396Gln | missense_variant | 13/25 | ENST00000326195.13 | |
ABCF1 | NM_001090.3 | c.1073G>A | p.Arg358Gln | missense_variant | 12/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCF1 | ENST00000326195.13 | c.1187G>A | p.Arg396Gln | missense_variant | 13/25 | 1 | NM_001025091.2 | A1 | |
ABCF1 | ENST00000376545.7 | c.1073G>A | p.Arg358Gln | missense_variant | 12/24 | 1 | |||
ABCF1 | ENST00000475993.1 | c.440G>A | p.Arg147Gln | missense_variant, NMD_transcript_variant | 5/18 | 1 | |||
ABCF1 | ENST00000441867.6 | c.1190G>A | p.Arg397Gln | missense_variant | 13/25 | 5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00480 AC: 730AN: 152114Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00125 AC: 309AN: 246460Hom.: 0 AF XY: 0.000864 AC XY: 116AN XY: 134328
GnomAD4 exome AF: 0.000511 AC: 747AN: 1460826Hom.: 4 Cov.: 32 AF XY: 0.000446 AC XY: 324AN XY: 726728
GnomAD4 genome AF: 0.00480 AC: 730AN: 152232Hom.: 9 Cov.: 32 AF XY: 0.00424 AC XY: 316AN XY: 74444
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 26, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at