rs6076347
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_021067.5(GINS1):c.289G>A(p.Val97Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 1,598,772 control chromosomes in the GnomAD database, including 158,124 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Synonymous variant affecting the same amino acid position (i.e. V97V) has been classified as Likely benign.
Frequency
Consequence
NM_021067.5 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 | UniProt |
---|---|---|---|---|---|---|---|
GINS1 | NM_021067.5 | c.289G>A | p.Val97Ile | missense_variant | 4/7 | ENST00000262460.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GINS1 | ENST00000262460.5 | c.289G>A | p.Val97Ile | missense_variant | 4/7 | 1 | NM_021067.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.350 AC: 53136AN: 151968Hom.: 10898 Cov.: 32
GnomAD3 exomes AF: 0.382 AC: 95925AN: 251376Hom.: 20970 AF XY: 0.389 AC XY: 52875AN XY: 135866
GnomAD4 exome AF: 0.439 AC: 634508AN: 1446686Hom.: 147221 Cov.: 28 AF XY: 0.437 AC XY: 315149AN XY: 720662
GnomAD4 genome AF: 0.349 AC: 53147AN: 152086Hom.: 10903 Cov.: 32 AF XY: 0.345 AC XY: 25626AN XY: 74336
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 13, 2019 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 65% of patients studied by a panel of primary immunodeficiencies. Number of patients: 62. Only high quality variants are reported. - |
Combined immunodeficiency due to GINS1 deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at