chr7-151223732-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_007189.3(ABCF2):c.668G>A(p.Arg223His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000158 in 1,612,356 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007189.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCF2 | NM_007189.3 | c.668G>A | p.Arg223His | missense_variant | 5/15 | ENST00000287844.7 | |
ABCF2-H2BK1 | NR_160983.1 | n.753G>A | non_coding_transcript_exon_variant | 5/17 | |||
ABCF2-H2BK1 | NM_005692.5 | c.668G>A | p.Arg223His | missense_variant | 5/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCF2 | ENST00000287844.7 | c.668G>A | p.Arg223His | missense_variant | 5/15 | 1 | NM_007189.3 | P1 | |
ABCF2 | ENST00000468073.5 | c.668G>A | p.Arg223His | missense_variant | 4/6 | 2 | |||
ABCF2 | ENST00000441774.1 | c.668G>A | p.Arg223His | missense_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000843 AC: 21AN: 249058Hom.: 0 AF XY: 0.0000891 AC XY: 12AN XY: 134656
GnomAD4 exome AF: 0.000162 AC: 237AN: 1460040Hom.: 1 Cov.: 31 AF XY: 0.000182 AC XY: 132AN XY: 725986
GnomAD4 genome AF: 0.000118 AC: 18AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 18, 2023 | The c.668G>A (p.R223H) alteration is located in exon 5 (coding exon 4) of the ABCF2 gene. This alteration results from a G to A substitution at nucleotide position 668, causing the arginine (R) at amino acid position 223 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at