chr1-156242577-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_199173.6(BGLAP):c.89C>A(p.Ser30Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0000187 in 1,554,052 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_199173.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152074Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000185 AC: 26AN: 1401978Hom.: 0 Cov.: 32 AF XY: 0.0000217 AC XY: 15AN XY: 691892
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74278
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.89C>A (p.S30Y) alteration is located in exon 2 (coding exon 2) of the BGLAP gene. This alteration results from a C to A substitution at nucleotide position 89, causing the serine (S) at amino acid position 30 to be replaced by a tyrosine (Y). 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