chr4-109463119-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_006323.5(SEC24B):āc.352A>Gā(p.Ser118Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,614,072 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_006323.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEC24B | NM_006323.5 | c.352A>G | p.Ser118Gly | missense_variant | 2/24 | ENST00000265175.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEC24B | ENST00000265175.5 | c.352A>G | p.Ser118Gly | missense_variant | 2/24 | 1 | NM_006323.5 | A2 | |
SEC24B | ENST00000504968.6 | c.445A>G | p.Ser149Gly | missense_variant | 3/25 | 1 | A2 | ||
SEC24B | ENST00000399100.6 | c.352A>G | p.Ser118Gly | missense_variant | 2/23 | 1 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249464Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135346
GnomAD4 exome AF: 0.0000417 AC: 61AN: 1461852Hom.: 0 Cov.: 35 AF XY: 0.0000316 AC XY: 23AN XY: 727232
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74386
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at