rs4461946
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015912.4(FAM135B):c.874-1615C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 151,968 control chromosomes in the GnomAD database, including 12,397 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 0.39 ( 12397 hom., cov: 32)
Consequence
FAM135B
NM_015912.4 intron
NM_015912.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.40
Genes affected
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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=-0.96).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM135B | NM_015912.4 | c.874-1615C>T | intron_variant | ENST00000395297.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM135B | ENST00000395297.6 | c.874-1615C>T | intron_variant | 5 | NM_015912.4 | P1 | |||
FAM135B | ENST00000482951.6 | c.*820-1615C>T | intron_variant, NMD_transcript_variant | 1 | |||||
FAM135B | ENST00000276737.10 | c.874-1615C>T | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.392 AC: 59498AN: 151850Hom.: 12358 Cov.: 32
GnomAD3 genomes
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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: 0.392 AC: 59589AN: 151968Hom.: 12397 Cov.: 32 AF XY: 0.386 AC XY: 28641AN XY: 74258
GnomAD4 genome
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28641
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74258
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1119
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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