chr4-69754675-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_014465.4(SULT1B1):c.272C>T(p.Thr91Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000992 in 1,612,192 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_014465.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SULT1B1 | NM_014465.4 | c.272C>T | p.Thr91Ile | missense_variant | 3/8 | ENST00000310613.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SULT1B1 | ENST00000310613.8 | c.272C>T | p.Thr91Ile | missense_variant | 3/8 | 1 | NM_014465.4 | P1 | |
SULT1B1 | ENST00000510821.1 | c.272C>T | p.Thr91Ile | missense_variant | 4/6 | 3 | |||
SULT1B1 | ENST00000512870.1 | c.215C>T | p.Thr72Ile | missense_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152066Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250182Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135304
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1460126Hom.: 0 Cov.: 31 AF XY: 0.00000964 AC XY: 7AN XY: 726340
GnomAD4 genome AF: 0.0000395 AC: 6AN: 152066Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74276
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 02, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at