rs2228314
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004599.4(SREBF2):āc.1784G>Cā(p.Gly595Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 1,613,924 control chromosomes in the GnomAD database, including 80,308 homozygotes. 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 Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004599.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SREBF2 | NM_004599.4 | c.1784G>C | p.Gly595Ala | missense_variant | 10/19 | ENST00000361204.9 | NP_004590.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SREBF2 | ENST00000361204.9 | c.1784G>C | p.Gly595Ala | missense_variant | 10/19 | 1 | NM_004599.4 | ENSP00000354476.4 | ||
SREBF2 | ENST00000424354.5 | n.1884G>C | non_coding_transcript_exon_variant | 11/22 | 1 | ENSP00000395728.1 | ||||
SREBF2 | ENST00000710853.1 | c.1694G>C | p.Gly565Ala | missense_variant | 10/19 | ENSP00000518526.1 |
Frequencies
GnomAD3 genomes AF: 0.373 AC: 56625AN: 151980Hom.: 12602 Cov.: 32
GnomAD3 exomes AF: 0.342 AC: 85601AN: 250568Hom.: 18269 AF XY: 0.326 AC XY: 44174AN XY: 135568
GnomAD4 exome AF: 0.290 AC: 424265AN: 1461824Hom.: 67669 Cov.: 53 AF XY: 0.290 AC XY: 210883AN XY: 727202
GnomAD4 genome AF: 0.373 AC: 56719AN: 152100Hom.: 12639 Cov.: 32 AF XY: 0.371 AC XY: 27588AN XY: 74354
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | This variant is associated with the following publications: (PMID: 22182810, 19740467, 12801623, 12119189, 28902428) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at