1-206931683-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002644.4(PIGR):c.2128G>A(p.Gly710Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000663 in 1,614,024 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002644.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000107 AC: 27AN: 251488Hom.: 0 AF XY: 0.000147 AC XY: 20AN XY: 135916
GnomAD4 exome AF: 0.0000657 AC: 96AN: 1461888Hom.: 0 Cov.: 33 AF XY: 0.0000853 AC XY: 62AN XY: 727246
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2128G>A (p.G710R) alteration is located in exon 9 (coding exon 8) of the PIGR gene. This alteration results from a G to A substitution at nucleotide position 2128, causing the glycine (G) at amino acid position 710 to be replaced by an arginine (R). 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