chr4-186138565-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001395294.1(FAM149A):c.567-10608C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,928 control chromosomes in the GnomAD database, including 10,092 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 0.36 ( 10092 hom., cov: 31)
Consequence
FAM149A
NM_001395294.1 intron
NM_001395294.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.63
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=-0.93).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM149A | NM_001395294.1 | c.567-10608C>T | intron_variant | ENST00000706927.1 | |||
FAM149A | NM_001367768.3 | c.567-10608C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM149A | ENST00000706927.1 | c.567-10608C>T | intron_variant | NM_001395294.1 | A2 | ||||
FAM149A | ENST00000389354.7 | c.567-10608C>T | intron_variant | 5 | A2 | ||||
FAM149A | ENST00000503432.5 | c.-307-10608C>T | intron_variant | 2 | P2 | ||||
FAM149A | ENST00000508379.5 | n.458-10608C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.358 AC: 54280AN: 151810Hom.: 10081 Cov.: 31
GnomAD3 genomes
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54280
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.358 AC: 54317AN: 151928Hom.: 10092 Cov.: 31 AF XY: 0.353 AC XY: 26204AN XY: 74248
GnomAD4 genome
?
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31
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26204
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74248
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Asia WGS
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1160
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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