16-71849931-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001137675.4(ATXN1L):c.191G>T(p.Gly64Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000011 in 1,551,108 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001137675.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATXN1L | NM_001137675.4 | c.191G>T | p.Gly64Val | missense_variant | 3/3 | ENST00000427980.7 | NP_001131147.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATXN1L | ENST00000427980.7 | c.191G>T | p.Gly64Val | missense_variant | 3/3 | 1 | NM_001137675.4 | ENSP00000415822 | P1 | |
ATXN1L | ENST00000683775.1 | c.191G>T | p.Gly64Val | missense_variant | 3/3 | ENSP00000507897 | P1 | |||
IST1 | ENST00000568581.5 | c.-16+1860G>T | intron_variant | 5 | ENSP00000456200 | |||||
ATXN1L | ENST00000569119.1 | n.119+1860G>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000261 AC: 4AN: 153288Hom.: 0 AF XY: 0.0000369 AC XY: 3AN XY: 81366
GnomAD4 exome AF: 0.0000114 AC: 16AN: 1398956Hom.: 0 Cov.: 30 AF XY: 0.0000130 AC XY: 9AN XY: 689918
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 15, 2023 | The c.191G>T (p.G64V) alteration is located in exon 3 (coding exon 1) of the ATXN1L gene. This alteration results from a G to T substitution at nucleotide position 191, causing the glycine (G) at amino acid position 64 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