rs3918001
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000373103.5(CSF3R):c.2047G>A(p.Gly683Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00906 in 1,613,922 control chromosomes in the GnomAD database, including 910 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
ENST00000373103.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CSF3R | NM_000760.4 | c.2041-75G>A | intron_variant | ENST00000373106.6 | NP_000751.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CSF3R | ENST00000373106.6 | c.2041-75G>A | intron_variant | 1 | NM_000760.4 | ENSP00000362198 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0443 AC: 6741AN: 152154Hom.: 483 Cov.: 33
GnomAD3 exomes AF: 0.0120 AC: 2944AN: 245468Hom.: 182 AF XY: 0.00930 AC XY: 1245AN XY: 133820
GnomAD4 exome AF: 0.00537 AC: 7856AN: 1461650Hom.: 425 Cov.: 31 AF XY: 0.00479 AC XY: 3483AN XY: 727132
GnomAD4 genome AF: 0.0444 AC: 6763AN: 152272Hom.: 485 Cov.: 33 AF XY: 0.0432 AC XY: 3220AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 11, 2021 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at