chr1-150842466-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM1BP4_Moderate
The NM_001668.4(ARNT):c.230C>T(p.Ser77Leu) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000163 in 1,591,164 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001668.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARNT | NM_001668.4 | c.230C>T | p.Ser77Leu | missense_variant, splice_region_variant | 5/22 | ENST00000358595.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARNT | ENST00000358595.10 | c.230C>T | p.Ser77Leu | missense_variant, splice_region_variant | 5/22 | 1 | NM_001668.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000269 AC: 4AN: 148764Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000805 AC: 2AN: 248446Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134618
GnomAD4 exome AF: 0.0000153 AC: 22AN: 1442400Hom.: 0 Cov.: 31 AF XY: 0.0000209 AC XY: 15AN XY: 717208
GnomAD4 genome ? AF: 0.0000269 AC: 4AN: 148764Hom.: 0 Cov.: 31 AF XY: 0.0000139 AC XY: 1AN XY: 72176
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 02, 2022 | The c.230C>T (p.S77L) alteration is located in exon 5 (coding exon 5) of the ARNT gene. This alteration results from a C to T substitution at nucleotide position 230, causing the serine (S) at amino acid position 77 to be replaced by a leucine (L). 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