chr5-32591670-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006713.4(SUB1):c.180T>A(p.Asp60Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000141 in 1,421,718 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006713.4 missense
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 |
---|---|---|---|---|---|---|---|
SUB1 | NM_006713.4 | c.180T>A | p.Asp60Glu | missense_variant | 3/5 | ENST00000265073.9 | |
SUB1 | XM_011513944.4 | c.180T>A | p.Asp60Glu | missense_variant | 4/6 | ||
SUB1 | XM_047416661.1 | c.180T>A | p.Asp60Glu | missense_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUB1 | ENST00000265073.9 | c.180T>A | p.Asp60Glu | missense_variant | 3/5 | 1 | NM_006713.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 1AN: 151450Hom.: 0 Cov.: 31 FAILED QC
GnomAD4 exome AF: 0.00000141 AC: 2AN: 1421718Hom.: 0 Cov.: 29 AF XY: 0.00000141 AC XY: 1AN XY: 706778
GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.00000660 AC: 1AN: 151450Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73926
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.180T>A (p.D60E) alteration is located in exon 3 (coding exon 2) of the SUB1 gene. This alteration results from a T to A substitution at nucleotide position 180, causing the aspartic acid (D) at amino acid position 60 to be replaced by a glutamic acid (E). 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