3-4979978-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003670.3(BHLHE40):āc.97A>Gā(p.Met33Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,614,016 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (ā ).
Frequency
Consequence
NM_003670.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BHLHE40 | NM_003670.3 | c.97A>G | p.Met33Val | missense_variant | 2/5 | ENST00000256495.4 | |
BHLHE40-AS1 | NR_125916.1 | upstream_gene_variant | |||||
BHLHE40-AS1 | NR_037903.3 | upstream_gene_variant | |||||
BHLHE40-AS1 | NR_125915.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BHLHE40 | ENST00000256495.4 | c.97A>G | p.Met33Val | missense_variant | 2/5 | 1 | NM_003670.3 | P1 | |
BHLHE40-AS1 | ENST00000668962.1 | n.437T>C | non_coding_transcript_exon_variant | 1/4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152156Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251444Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135914
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461860Hom.: 1 Cov.: 32 AF XY: 0.0000165 AC XY: 12AN XY: 727232
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152156Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 15, 2023 | The c.97A>G (p.M33V) alteration is located in exon 2 (coding exon 2) of the BHLHE40 gene. This alteration results from a A to G substitution at nucleotide position 97, causing the methionine (M) at amino acid position 33 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