X-1282786-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_172245.4(CSF2RA):c.76+7A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,612,546 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 13 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_172245.4 splice_region, intron
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 |
---|---|---|---|---|---|---|---|
CSF2RA | NM_172245.4 | c.76+7A>G | splice_region_variant, intron_variant | ENST00000381529.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSF2RA | ENST00000381529.9 | c.76+7A>G | splice_region_variant, intron_variant | 1 | NM_172245.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152080Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74278
GnomAD3 exomes AF: 0.0000876 AC: 22AN: 251178Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135742
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1460466Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 12AN XY: 726616
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152080Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74278
ClinVar
Submissions by phenotype
Surfactant metabolism dysfunction, pulmonary, 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at