12-26122619-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_030762.3(BHLHE41):c.896C>T(p.Ala299Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,167,938 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_030762.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BHLHE41 | NM_030762.3 | c.896C>T | p.Ala299Val | missense_variant | 5/5 | ENST00000242728.5 | |
SSPN | XM_011520853.4 | c.-31+467G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BHLHE41 | ENST00000242728.5 | c.896C>T | p.Ala299Val | missense_variant | 5/5 | 1 | NM_030762.3 | P1 | |
SSPN | ENST00000538142.5 | c.-31+467G>A | intron_variant | 4 | |||||
SSPN | ENST00000534829.5 | n.101+467G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000206 AC: 3AN: 145924Hom.: 0 Cov.: 30
GnomAD4 exome AF: 0.0000205 AC: 21AN: 1022014Hom.: 0 Cov.: 29 AF XY: 0.0000144 AC XY: 7AN XY: 485504
GnomAD4 genome ? AF: 0.0000206 AC: 3AN: 145924Hom.: 0 Cov.: 30 AF XY: 0.0000141 AC XY: 1AN XY: 71022
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 14, 2023 | The c.896C>T (p.A299V) alteration is located in exon 5 (coding exon 5) of the BHLHE41 gene. This alteration results from a C to T substitution at nucleotide position 896, causing the alanine (A) at amino acid position 299 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