7-128677605-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001128926.4(GARIN1A):c.380G>A(p.Arg127Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000968 in 1,612,860 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001128926.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GARIN1A | NM_001128926.4 | c.380G>A | p.Arg127Gln | missense_variant | 3/5 | ENST00000682356.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GARIN1A | ENST00000682356.1 | c.380G>A | p.Arg127Gln | missense_variant | 3/5 | NM_001128926.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000732 AC: 111AN: 151730Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000600 AC: 149AN: 248338Hom.: 0 AF XY: 0.000542 AC XY: 73AN XY: 134752
GnomAD4 exome AF: 0.000993 AC: 1451AN: 1461036Hom.: 1 Cov.: 38 AF XY: 0.000974 AC XY: 708AN XY: 726756
GnomAD4 genome AF: 0.000731 AC: 111AN: 151824Hom.: 0 Cov.: 31 AF XY: 0.000661 AC XY: 49AN XY: 74180
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 22, 2021 | The c.407G>A (p.R136Q) alteration is located in exon 3 (coding exon 3) of the FAM71F2 gene. This alteration results from a G to A substitution at nucleotide position 407, causing the arginine (R) at amino acid position 136 to be replaced by a glutamine (Q). 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