chr12-99648206-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_153364.4(GARIN6):c.32C>T(p.Thr11Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,613,966 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153364.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GARIN6 | NM_153364.4 | c.32C>T | p.Thr11Met | missense_variant | 1/2 | ENST00000324341.2 | |
ANKS1B | NM_001352186.2 | c.1272+6861G>A | intron_variant | ENST00000683438.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GARIN6 | ENST00000324341.2 | c.32C>T | p.Thr11Met | missense_variant | 1/2 | 1 | NM_153364.4 | P1 | |
ANKS1B | ENST00000683438.2 | c.1272+6861G>A | intron_variant | NM_001352186.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251024Hom.: 0 AF XY: 0.0000664 AC XY: 9AN XY: 135636
GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461794Hom.: 0 Cov.: 35 AF XY: 0.0000413 AC XY: 30AN XY: 727188
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.32C>T (p.T11M) alteration is located in exon 1 (coding exon 1) of the FAM71C gene. This alteration results from a C to T substitution at nucleotide position 32, causing the threonine (T) at amino acid position 11 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