chr19-48587291-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_177973.2(SULT2B1):c.277C>T(p.Arg93Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000722 in 1,614,032 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R93H) has been classified as Uncertain significance.
Frequency
Consequence
NM_177973.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SULT2B1 | NM_177973.2 | c.277C>T | p.Arg93Cys | missense_variant | 3/7 | ENST00000201586.7 | |
SULT2B1 | NM_004605.2 | c.232C>T | p.Arg78Cys | missense_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SULT2B1 | ENST00000201586.7 | c.277C>T | p.Arg93Cys | missense_variant | 3/7 | 1 | NM_177973.2 | P2 | |
SULT2B1 | ENST00000323090.4 | c.232C>T | p.Arg78Cys | missense_variant | 2/6 | 1 | A2 | ||
ENST00000666424.1 | n.493+9455G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000546 AC: 83AN: 152038Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000948 AC: 238AN: 251010Hom.: 2 AF XY: 0.00122 AC XY: 165AN XY: 135674
GnomAD4 exome AF: 0.000740 AC: 1082AN: 1461876Hom.: 6 Cov.: 31 AF XY: 0.000869 AC XY: 632AN XY: 727240
GnomAD4 genome AF: 0.000545 AC: 83AN: 152156Hom.: 0 Cov.: 31 AF XY: 0.000551 AC XY: 41AN XY: 74388
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | SULT2B1: BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at