4-6716337-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018366.3(BLOC1S4):c.128C>T(p.Pro43Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000404 in 1,236,220 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_018366.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151668Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000277 AC: 3AN: 1084552Hom.: 0 Cov.: 31 AF XY: 0.00000389 AC XY: 2AN XY: 513764
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151668Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74046
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.128C>T (p.P43L) alteration is located in exon 1 (coding exon 1) of the BLOC1S4 gene. This alteration results from a C to T substitution at nucleotide position 128, causing the proline (P) at amino acid position 43 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