chr8-138151603-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_015912.4(FAM135B):c.2872G>A(p.Gly958Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 1,614,142 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_015912.4 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 |
---|---|---|---|---|---|---|---|
FAM135B | NM_015912.4 | c.2872G>A | p.Gly958Ser | missense_variant | 13/20 | ENST00000395297.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM135B | ENST00000395297.6 | c.2872G>A | p.Gly958Ser | missense_variant | 13/20 | 5 | NM_015912.4 | P1 | |
FAM135B | ENST00000467365.2 | n.802G>A | non_coding_transcript_exon_variant | 1/4 | 1 | ||||
FAM135B | ENST00000482951.6 | c.*2818G>A | 3_prime_UTR_variant, NMD_transcript_variant | 14/21 | 1 | ||||
FAM135B | ENST00000276737.10 | c.2872G>A | p.Gly958Ser | missense_variant, NMD_transcript_variant | 13/20 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000479 AC: 12AN: 250572Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135404
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1461824Hom.: 0 Cov.: 29 AF XY: 0.0000426 AC XY: 31AN XY: 727214
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152318Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74476
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at