chr4-47320173-T-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_000812.4(GABRB1):c.508T>C(p.Leu170=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.986 in 1,607,758 control chromosomes in the GnomAD database, including 781,536 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. L170L) has been classified as Likely benign.
Frequency
Consequence
NM_000812.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRB1 | NM_000812.4 | c.508T>C | p.Leu170= | synonymous_variant | 5/9 | ENST00000295454.8 | |
GABRB1 | XM_024453976.2 | c.409T>C | p.Leu137= | synonymous_variant | 5/9 | ||
GABRB1 | XM_024453977.2 | c.409T>C | p.Leu137= | synonymous_variant | 6/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRB1 | ENST00000295454.8 | c.508T>C | p.Leu170= | synonymous_variant | 5/9 | 1 | NM_000812.4 | P1 | |
GABRB1 | ENST00000510909.1 | c.*176T>C | 3_prime_UTR_variant, NMD_transcript_variant | 4/5 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.970 AC: 147638AN: 152190Hom.: 71710 Cov.: 31
GnomAD3 exomes AF: 0.986 AC: 247796AN: 251420Hom.: 122160 AF XY: 0.987 AC XY: 134069AN XY: 135878
GnomAD4 exome AF: 0.987 AC: 1437241AN: 1455450Hom.: 709777 Cov.: 35 AF XY: 0.988 AC XY: 715692AN XY: 724532
GnomAD4 genome ? AF: 0.970 AC: 147744AN: 152308Hom.: 71759 Cov.: 31 AF XY: 0.971 AC XY: 72303AN XY: 74460
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at