chr9-68780561-T-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_138333.5(PABIR1):c.397T>A(p.Ser133Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000222 in 1,613,980 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S133C) has been classified as Uncertain significance.
Frequency
Consequence
NM_138333.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PABIR1 | NM_138333.5 | c.397T>A | p.Ser133Thr | missense_variant | 1/1 | ENST00000394264.7 | |
PIP5K1B | NM_003558.4 | c.-85-37900T>A | intron_variant | ENST00000265382.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PABIR1 | ENST00000394264.7 | c.397T>A | p.Ser133Thr | missense_variant | 1/1 | NM_138333.5 | P1 | ||
PIP5K1B | ENST00000265382.8 | c.-85-37900T>A | intron_variant | 1 | NM_003558.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000270 AC: 41AN: 152090Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000410 AC: 103AN: 251456Hom.: 0 AF XY: 0.000427 AC XY: 58AN XY: 135900
GnomAD4 exome AF: 0.000218 AC: 318AN: 1461890Hom.: 3 Cov.: 31 AF XY: 0.000215 AC XY: 156AN XY: 727244
GnomAD4 genome ? AF: 0.000270 AC: 41AN: 152090Hom.: 0 Cov.: 33 AF XY: 0.000269 AC XY: 20AN XY: 74288
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The c.397T>A (p.S133T) alteration is located in exon 1 (coding exon 1) of the FAM122A gene. This alteration results from a T to A substitution at nucleotide position 397, causing the serine (S) at amino acid position 133 to be replaced by a threonine (T). 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