17-42583541-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_178126.4(RETREG3):c.767A>G(p.Asn256Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,613,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178126.4 missense
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 |
---|---|---|---|---|---|---|---|
RETREG3 | NM_178126.4 | c.767A>G | p.Asn256Ser | missense_variant | 7/9 | ENST00000309428.10 | |
RETREG3 | XM_047435503.1 | c.476A>G | p.Asn159Ser | missense_variant | 8/10 | ||
RETREG3 | NR_026697.2 | n.839A>G | non_coding_transcript_exon_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RETREG3 | ENST00000309428.10 | c.767A>G | p.Asn256Ser | missense_variant | 7/9 | 1 | NM_178126.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251456Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135898
GnomAD4 exome AF: 0.0000369 AC: 54AN: 1461580Hom.: 0 Cov.: 31 AF XY: 0.0000523 AC XY: 38AN XY: 727098
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152308Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 19, 2023 | The c.767A>G (p.N256S) alteration is located in exon 7 (coding exon 7) of the FAM134C gene. This alteration results from a A to G substitution at nucleotide position 767, causing the asparagine (N) at amino acid position 256 to be replaced by a serine (S). 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