chr7-135246572-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001394401.1(STRA8):c.749C>T(p.Ala250Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000979 in 1,552,274 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001394401.1 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 |
---|---|---|---|---|---|---|---|
STRA8 | NM_001394401.1 | c.749C>T | p.Ala250Val | missense_variant | 6/9 | ENST00000662584.2 | |
STRA8 | NM_182489.3 | c.536C>T | p.Ala179Val | missense_variant | 6/9 | ||
STRA8 | XM_011516137.3 | c.749C>T | p.Ala250Val | missense_variant | 5/8 | ||
STRA8 | XM_047420324.1 | c.749C>T | p.Ala250Val | missense_variant | 6/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STRA8 | ENST00000662584.2 | c.749C>T | p.Ala250Val | missense_variant | 6/9 | NM_001394401.1 | P2 | ||
STRA8 | ENST00000275764.3 | c.602C>T | p.Ala201Val | missense_variant | 6/9 | 1 | A2 | ||
ENST00000637483.1 | n.730G>A | non_coding_transcript_exon_variant | 5/5 | 5 | |||||
STRA8 | ENST00000667288.1 | c.536C>T | p.Ala179Val | missense_variant | 6/9 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000298 AC: 44AN: 147504Hom.: 0 AF XY: 0.000275 AC XY: 22AN XY: 80008
GnomAD4 exome AF: 0.0000943 AC: 132AN: 1400138Hom.: 0 Cov.: 31 AF XY: 0.0000911 AC XY: 63AN XY: 691330
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 05, 2021 | The c.602C>T (p.A201V) alteration is located in exon 6 (coding exon 6) of the STRA8 gene. This alteration results from a C to T substitution at nucleotide position 602, causing the alanine (A) at amino acid position 201 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