6-3127284-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004332.4(BPHL):āc.254A>Gā(p.Asn85Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000251 in 1,595,866 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004332.4 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: 0.0000921 AC: 14AN: 151938Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000447 AC: 11AN: 245812Hom.: 0 AF XY: 0.0000301 AC XY: 4AN XY: 133102
GnomAD4 exome AF: 0.0000180 AC: 26AN: 1443928Hom.: 0 Cov.: 30 AF XY: 0.0000181 AC XY: 13AN XY: 718544
GnomAD4 genome AF: 0.0000921 AC: 14AN: 151938Hom.: 0 Cov.: 30 AF XY: 0.0000674 AC XY: 5AN XY: 74184
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 25, 2023 | The c.254A>G (p.N85S) alteration is located in exon 3 (coding exon 3) of the BPHL gene. This alteration results from a A to G substitution at nucleotide position 254, causing the asparagine (N) at amino acid position 85 to be replaced by a serine (S). 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