chr4-76179549-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_005506.4(SCARB2):c.580G>A(p.Asp194Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,614,044 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. D194D) has been classified as Likely benign.
Frequency
Consequence
NM_005506.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCARB2 | NM_005506.4 | c.580G>A | p.Asp194Asn | missense_variant | 4/12 | ENST00000264896.8 | |
SCARB2 | XM_047416429.1 | c.106G>A | p.Asp36Asn | missense_variant | 4/12 | ||
SCARB2 | XM_047416430.1 | c.106G>A | p.Asp36Asn | missense_variant | 4/12 | ||
SCARB2 | NM_001204255.2 | c.276-3639G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCARB2 | ENST00000264896.8 | c.580G>A | p.Asp194Asn | missense_variant | 4/12 | 1 | NM_005506.4 | P4 | |
ENST00000651366.1 | n.103-20417C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152142Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000175 AC: 44AN: 251378Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135858
GnomAD4 exome AF: 0.0000328 AC: 48AN: 1461784Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727206
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152260Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74436
ClinVar
Submissions by phenotype
Action myoclonus-renal failure syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Mar 12, 2020 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Mar 25, 2019 | Has not been previously published as pathogenic or benign to our knowledge; In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function - |
Progressive myoclonic epilepsy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 29, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at