6-8041169-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_201280.3(BLOC1S5):c.295C>T(p.Arg99Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,608,534 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_201280.3 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 |
---|---|---|---|---|---|---|---|
BLOC1S5 | NM_201280.3 | c.295C>T | p.Arg99Trp | missense_variant | 3/5 | ENST00000397457.7 | |
BLOC1S5-TXNDC5 | NR_037616.1 | n.333C>T | non_coding_transcript_exon_variant | 3/13 | |||
EEF1E1-BLOC1S5 | NR_037618.1 | n.641C>T | non_coding_transcript_exon_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BLOC1S5 | ENST00000397457.7 | c.295C>T | p.Arg99Trp | missense_variant | 3/5 | 1 | NM_201280.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152044Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000283 AC: 7AN: 247304Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133436
GnomAD4 exome AF: 0.00000687 AC: 10AN: 1456490Hom.: 0 Cov.: 31 AF XY: 0.00000552 AC XY: 4AN XY: 724226
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152044Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74252
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.295C>T (p.R99W) alteration is located in exon 3 (coding exon 3) of the BLOC1S5 gene. This alteration results from a C to T substitution at nucleotide position 295, causing the arginine (R) at amino acid position 99 to be replaced by a tryptophan (W). 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