rs6997
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022171.3(TCTA):c.*1539C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 261,562 control chromosomes in the GnomAD database, including 11,879 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 0.30 ( 7228 hom., cov: 32)
Exomes 𝑓: 0.27 ( 4651 hom. )
Consequence
TCTA
NM_022171.3 3_prime_UTR
NM_022171.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.350
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=-0.79).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCTA | NM_022171.3 | c.*1539C>T | 3_prime_UTR_variant | 3/3 | ENST00000273590.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCTA | ENST00000273590.4 | c.*1539C>T | 3_prime_UTR_variant | 3/3 | 1 | NM_022171.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.298 AC: 45243AN: 152072Hom.: 7220 Cov.: 32
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GnomAD4 exome AF: 0.273 AC: 29831AN: 109372Hom.: 4651 Cov.: 0 AF XY: 0.267 AC XY: 15568AN XY: 58336
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GnomAD4 genome ? AF: 0.297 AC: 45274AN: 152190Hom.: 7228 Cov.: 32 AF XY: 0.300 AC XY: 22285AN XY: 74400
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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
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