rs2116519
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001017961.5(FAM78B):c.263+5005C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,074 control chromosomes in the GnomAD database, including 30,494 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 0.61 ( 30494 hom., cov: 32)
Consequence
FAM78B
NM_001017961.5 intron
NM_001017961.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.637
Genes affected
FAM78B (HGNC:13495): (family with sequence similarity 78 member B)
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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=-0.86).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM78B | NM_001017961.5 | c.263+5005C>T | intron_variant | ENST00000354422.4 | |||
FAM78B | NM_001320302.2 | c.263+5005C>T | intron_variant | ||||
FAM78B | NR_135199.2 | n.1016+5005C>T | intron_variant, non_coding_transcript_variant | ||||
FAM78B | NR_163271.1 | n.770+5005C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM78B | ENST00000354422.4 | c.263+5005C>T | intron_variant | 2 | NM_001017961.5 | P1 | |||
ENST00000451784.1 | n.306+3809C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.615 AC: 93425AN: 151956Hom.: 30488 Cov.: 32
GnomAD3 genomes
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151956
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.615 AC: 93459AN: 152074Hom.: 30494 Cov.: 32 AF XY: 0.611 AC XY: 45445AN XY: 74320
GnomAD4 genome
?
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93459
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152074
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32
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45445
AN XY:
74320
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1799
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at