rs2536163
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014888.3(FAM3C):c.382+41G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 1,124,474 control chromosomes in the GnomAD database, including 25,614 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.25 ( 5872 hom., cov: 32)
Exomes 𝑓: 0.19 ( 19742 hom. )
Consequence
FAM3C
NM_014888.3 intron
NM_014888.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.378
Genes affected
FAM3C (HGNC:18664): (FAM3 metabolism regulating signaling molecule C) This gene is a member of the family with sequence similarity 3 (FAM3) family and encodes a secreted protein with a GG domain. A change in expression of this protein has been noted in pancreatic cancer-derived cells. [provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM3C | NM_014888.3 | c.382+41G>A | intron_variant | ENST00000359943.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM3C | ENST00000359943.8 | c.382+41G>A | intron_variant | 1 | NM_014888.3 | P1 | |||
FAM3C | ENST00000412653.5 | c.382+41G>A | intron_variant | 4 | |||||
FAM3C | ENST00000426156.1 | c.292+41G>A | intron_variant | 5 | |||||
FAM3C | ENST00000497622.1 | n.515G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.254 AC: 38632AN: 151920Hom.: 5855 Cov.: 32
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GnomAD3 exomes AF: 0.192 AC: 45212AN: 235748Hom.: 5031 AF XY: 0.189 AC XY: 24129AN XY: 127806
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GnomAD4 exome AF: 0.192 AC: 186465AN: 972436Hom.: 19742 Cov.: 13 AF XY: 0.192 AC XY: 96732AN XY: 504560
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GnomAD4 genome ? AF: 0.254 AC: 38689AN: 152038Hom.: 5872 Cov.: 32 AF XY: 0.250 AC XY: 18564AN XY: 74318
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at