rs2276919
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001395294.1(FAM149A):c.1602+174A>G variant causes a intron change. The variant allele was found at a frequency of 0.688 in 1,534,524 control chromosomes in the GnomAD database, including 366,389 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 0.65 ( 32362 hom., cov: 34)
Exomes 𝑓: 0.69 ( 334027 hom. )
Consequence
FAM149A
NM_001395294.1 intron
NM_001395294.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.37
Genes affected
FAM149A (HGNC:24527): (family with sequence similarity 149 member A)
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM149A | NM_001395294.1 | c.1602+174A>G | intron_variant | ENST00000706927.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM149A | ENST00000706927.1 | c.1602+174A>G | intron_variant | NM_001395294.1 | A2 | ||||
RPSAP70 | ENST00000504462.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.648 AC: 98543AN: 152018Hom.: 32342 Cov.: 34
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GnomAD3 exomes AF: 0.629 AC: 88317AN: 140410Hom.: 28287 AF XY: 0.638 AC XY: 48475AN XY: 76022
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GnomAD4 exome AF: 0.693 AC: 957371AN: 1382388Hom.: 334027 Cov.: 35 AF XY: 0.691 AC XY: 471628AN XY: 682428
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GnomAD4 genome ? AF: 0.648 AC: 98608AN: 152136Hom.: 32362 Cov.: 34 AF XY: 0.642 AC XY: 47739AN XY: 74362
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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