chr16-28606849-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001055.4(SULT1A1):c.506A>G(p.Tyr169Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,612,376 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y169F) has been classified as Uncertain significance.
Frequency
Consequence
NM_001055.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SULT1A1 | NM_001055.4 | c.506A>G | p.Tyr169Cys | missense_variant | 6/8 | ENST00000314752.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SULT1A1 | ENST00000314752.12 | c.506A>G | p.Tyr169Cys | missense_variant | 6/8 | 1 | NM_001055.4 | P1 | |
SULT1A1 | ENST00000569554.5 | c.506A>G | p.Tyr169Cys | missense_variant | 5/7 | 1 | P1 | ||
SULT1A1 | ENST00000566189.5 | c.506A>G | p.Tyr169Cys | missense_variant | 6/8 | 5 | |||
SULT1A1 | ENST00000567512.1 | c.380A>G | p.Tyr127Cys | missense_variant | 5/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151866Hom.: 0 Cov.: 36
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251210Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135770
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1460510Hom.: 1 Cov.: 90 AF XY: 0.0000206 AC XY: 15AN XY: 726586
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151866Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 74174
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 26, 2023 | The c.506A>G (p.Y169C) alteration is located in exon 6 (coding exon 5) of the SULT1A1 gene. This alteration results from a A to G substitution at nucleotide position 506, causing the tyrosine (Y) at amino acid position 169 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at