6-149578869-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138785.5(GINM1):āc.325A>Gā(p.Ile109Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000239 in 1,591,980 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (ā ).
Frequency
Consequence
NM_138785.5 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 |
---|---|---|---|---|---|---|---|
GINM1 | NM_138785.5 | c.325A>G | p.Ile109Val | missense_variant | 4/8 | ENST00000367419.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GINM1 | ENST00000367419.10 | c.325A>G | p.Ile109Val | missense_variant | 4/8 | 1 | NM_138785.5 | P1 | |
ENST00000627304.1 | n.220-653T>C | intron_variant, non_coding_transcript_variant | 5 | ||||||
GINM1 | ENST00000650599.1 | c.325A>G | p.Ile109Val | missense_variant, NMD_transcript_variant | 4/8 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000498 AC: 12AN: 240822Hom.: 0 AF XY: 0.0000231 AC XY: 3AN XY: 130046
GnomAD4 exome AF: 0.0000118 AC: 17AN: 1439704Hom.: 0 Cov.: 27 AF XY: 0.0000112 AC XY: 8AN XY: 716638
GnomAD4 genome AF: 0.000138 AC: 21AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 01, 2021 | The c.325A>G (p.I109V) alteration is located in exon 4 (coding exon 4) of the GINM1 gene. This alteration results from a A to G substitution at nucleotide position 325, causing the isoleucine (I) at amino acid position 109 to be replaced by a valine (V). 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