rs2262274
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_145306.3(FAM241B):c.96+112C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 151,912 control chromosomes in the GnomAD database, including 34,088 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 0.67 ( 34088 hom., cov: 31)
Exomes 𝑓: 0.68 ( 296954 hom. )
Failed GnomAD Quality Control
Consequence
FAM241B
NM_145306.3 intron
NM_145306.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.727
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=-0.83).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM241B | NM_145306.3 | c.96+112C>T | intron_variant | ENST00000373279.6 | |||
FAM241B | XM_005269606.3 | c.222+112C>T | intron_variant | ||||
FAM241B | XM_005269608.4 | c.96+112C>T | intron_variant | ||||
FAM241B | XM_011539455.3 | c.96+112C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM241B | ENST00000373279.6 | c.96+112C>T | intron_variant | 1 | NM_145306.3 | P1 | |||
FAM241B | ENST00000421716.1 | c.222+112C>T | intron_variant | 2 | |||||
FAM241B | ENST00000491890.1 | n.423+112C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.667 AC: 101190AN: 151794Hom.: 34051 Cov.: 31
GnomAD3 genomes
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.681 AC: 864344AN: 1269930Hom.: 296954 AF XY: 0.680 AC XY: 425003AN XY: 625360
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? AF: 0.667 AC: 101285AN: 151912Hom.: 34088 Cov.: 31 AF XY: 0.665 AC XY: 49392AN XY: 74272
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2725
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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