chr4-69844314-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005420.3(SULT1E1):āc.619A>Gā(p.Ile207Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,348 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 Uncertain significance (ā ).
Frequency
Consequence
NM_005420.3 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 |
---|---|---|---|---|---|---|---|
SULT1E1 | NM_005420.3 | c.619A>G | p.Ile207Val | missense_variant | 7/8 | ENST00000226444.4 | |
SULT1E1 | XM_047416100.1 | c.619A>G | p.Ile207Val | missense_variant | 6/7 | ||
SULT1E1 | XM_047416101.1 | c.619A>G | p.Ile207Val | missense_variant | 7/8 | ||
SULT1E1 | XR_007057952.1 | n.725A>G | non_coding_transcript_exon_variant | 7/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SULT1E1 | ENST00000226444.4 | c.619A>G | p.Ile207Val | missense_variant | 7/8 | 1 | NM_005420.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 250842Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135572
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1461178Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726852
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 27, 2022 | The c.619A>G (p.I207V) alteration is located in exon 7 (coding exon 6) of the SULT1E1 gene. This alteration results from a A to G substitution at nucleotide position 619, causing the isoleucine (I) at amino acid position 207 to be replaced by a valine (V). 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