16-1984275-G-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_005262.3(GFER):āc.57G>Cā(p.Pro19Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00113 in 1,477,164 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_005262.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GFER | ENST00000248114.7 | c.57G>C | p.Pro19Pro | synonymous_variant | Exon 1 of 3 | 1 | NM_005262.3 | ENSP00000248114.6 | ||
GFER | ENST00000561710.1 | c.18G>C | p.Pro6Pro | synonymous_variant | Exon 1 of 2 | 2 | ENSP00000456189.1 | |||
GFER | ENST00000569451.1 | c.57G>C | p.Pro19Pro | synonymous_variant | Exon 1 of 2 | 5 | ENSP00000456432.1 |
Frequencies
GnomAD3 genomes AF: 0.00585 AC: 890AN: 152032Hom.: 6 Cov.: 33
GnomAD3 exomes AF: 0.000665 AC: 54AN: 81174Hom.: 1 AF XY: 0.000580 AC XY: 27AN XY: 46580
GnomAD4 exome AF: 0.000577 AC: 765AN: 1325024Hom.: 8 Cov.: 32 AF XY: 0.000489 AC XY: 319AN XY: 652762
GnomAD4 genome AF: 0.00590 AC: 897AN: 152140Hom.: 6 Cov.: 33 AF XY: 0.00532 AC XY: 396AN XY: 74394
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
GFER-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at