rs10416551
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014173.4(BABAM1):c.700-47G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00443 in 1,570,410 control chromosomes in the GnomAD database, including 244 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 0.023 ( 135 hom., cov: 32)
Exomes 𝑓: 0.0024 ( 109 hom. )
Consequence
BABAM1
NM_014173.4 intron
NM_014173.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.177
Genes affected
BABAM1 (HGNC:25008): (BRISC and BRCA1 A complex member 1) Involved in several processes, including mitotic G2 DNA damage checkpoint signaling; positive regulation of DNA repair; and protein K63-linked deubiquitination. Located in cytosol and nuclear body. Part of BRCA1-A complex and BRISC complex. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.82).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0775 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BABAM1 | NM_014173.4 | c.700-47G>A | intron_variant | ENST00000598188.6 | |||
BABAM1 | NM_001033549.3 | c.700-47G>A | intron_variant | ||||
BABAM1 | NM_001288756.2 | c.700-47G>A | intron_variant | ||||
BABAM1 | NM_001288757.2 | c.475-47G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BABAM1 | ENST00000598188.6 | c.700-47G>A | intron_variant | 1 | NM_014173.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0231 AC: 3512AN: 152178Hom.: 134 Cov.: 32
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GnomAD3 exomes AF: 0.00547 AC: 1026AN: 187706Hom.: 38 AF XY: 0.00440 AC XY: 443AN XY: 100758
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GnomAD4 exome AF: 0.00243 AC: 3447AN: 1418114Hom.: 109 Cov.: 31 AF XY: 0.00208 AC XY: 1457AN XY: 702076
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GnomAD4 genome ? AF: 0.0231 AC: 3517AN: 152296Hom.: 135 Cov.: 32 AF XY: 0.0222 AC XY: 1653AN XY: 74478
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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