22-41873846-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_004599.4(SREBF2):c.916A>G(p.Met306Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000558 in 1,613,006 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M306T) has been classified as Uncertain significance.
Frequency
Consequence
NM_004599.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SREBF2 | NM_004599.4 | c.916A>G | p.Met306Val | missense_variant | 5/19 | ENST00000361204.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SREBF2 | ENST00000361204.9 | c.916A>G | p.Met306Val | missense_variant | 5/19 | 1 | NM_004599.4 | P3 | |
SREBF2 | ENST00000424354.5 | c.916A>G | p.Met306Val | missense_variant, NMD_transcript_variant | 5/22 | 1 | |||
SREBF2 | ENST00000710853.1 | c.826A>G | p.Met276Val | missense_variant | 5/19 | A2 | |||
SREBF2 | ENST00000462539.1 | n.158A>G | non_coding_transcript_exon_variant | 1/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249476Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134822
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460804Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726592
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 04, 2023 | The c.916A>G (p.M306V) alteration is located in exon 5 (coding exon 5) of the SREBF2 gene. This alteration results from a A to G substitution at nucleotide position 916, causing the methionine (M) at amino acid position 306 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