chr2-96894044-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001122646.3(FAM178B):c.1658C>T(p.Ser553Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000323 in 1,608,688 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001122646.3 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 |
---|---|---|---|---|---|---|---|
FAM178B | NM_001122646.3 | c.1658C>T | p.Ser553Leu | missense_variant | 14/17 | ENST00000490605.3 | |
FAM178B | NM_001172667.2 | c.35C>T | p.Ser12Leu | missense_variant | 2/5 | ||
FAM178B | NM_016490.5 | c.-23C>T | 5_prime_UTR_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM178B | ENST00000490605.3 | c.1658C>T | p.Ser553Leu | missense_variant | 14/17 | 5 | NM_001122646.3 | P1 | |
FAM178B | ENST00000393526.6 | c.-23C>T | 5_prime_UTR_variant | 2/5 | 1 | ||||
FAM178B | ENST00000470789.5 | n.90C>T | non_coding_transcript_exon_variant | 2/5 | 1 | ||||
FAM178B | ENST00000494172.1 | n.110C>T | non_coding_transcript_exon_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152034Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000165 AC: 4AN: 242012Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131218
GnomAD4 exome AF: 0.0000336 AC: 49AN: 1456654Hom.: 0 Cov.: 32 AF XY: 0.0000221 AC XY: 16AN XY: 724288
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152034Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74262
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 31, 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