rs2070929
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001290403.2(TAL1):c.*1785C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 396,002 control chromosomes in the GnomAD database, including 16,589 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 0.25 ( 5151 hom., cov: 32)
Exomes 𝑓: 0.29 ( 11438 hom. )
Consequence
TAL1
NM_001290403.2 3_prime_UTR
NM_001290403.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.04
Genes affected
TAL1 (HGNC:11556): (TAL bHLH transcription factor 1, erythroid differentiation factor) Enables several functions, including DNA-binding transcription factor activity; E-box binding activity; and histone deacetylase binding activity. Involved in several processes, including myeloid cell differentiation; positive regulation of cellular component organization; and positive regulation of erythrocyte differentiation. Located in chromatin and nucleoplasm. Part of transcription regulator complex. Implicated in acute lymphoblastic leukemia. [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=-0.83).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAL1 | NM_001290403.2 | c.*1785C>G | 3_prime_UTR_variant | 5/5 | ENST00000691006.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAL1 | ENST00000691006.1 | c.*1785C>G | 3_prime_UTR_variant | 5/5 | NM_001290403.2 | P1 | |||
TAL1 | ENST00000294339.3 | c.*1785C>G | 3_prime_UTR_variant | 4/4 | 1 | P1 | |||
TAL1 | ENST00000371884.6 | c.*1785C>G | 3_prime_UTR_variant | 5/5 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.251 AC: 38141AN: 151982Hom.: 5161 Cov.: 32
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GnomAD4 exome AF: 0.291 AC: 70992AN: 243902Hom.: 11438 Cov.: 0 AF XY: 0.290 AC XY: 35899AN XY: 123642
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GnomAD4 genome ? AF: 0.251 AC: 38118AN: 152100Hom.: 5151 Cov.: 32 AF XY: 0.251 AC XY: 18649AN XY: 74338
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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