12-99648787-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153364.4(GARIN6):c.613G>A(p.Val205Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000249 in 1,609,052 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153364.4 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
GARIN6 | NM_153364.4 | c.613G>A | p.Val205Met | missense_variant, splice_region_variant | 1/2 | ENST00000324341.2 | |
ANKS1B | NM_001352186.2 | c.1272+6280C>T | intron_variant | ENST00000683438.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GARIN6 | ENST00000324341.2 | c.613G>A | p.Val205Met | missense_variant, splice_region_variant | 1/2 | 1 | NM_153364.4 | P1 | |
ANKS1B | ENST00000683438.2 | c.1272+6280C>T | intron_variant | NM_001352186.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000407 AC: 1AN: 245600Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132706
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1456862Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 724046
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.613G>A (p.V205M) alteration is located in exon 1 (coding exon 1) of the FAM71C gene. This alteration results from a G to A substitution at nucleotide position 613, causing the valine (V) at amino acid position 205 to be replaced by a methionine (M). 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