rs750898498
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005458.8(GABBR2):c.2229+8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000299 in 1,605,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_005458.8 splice_region, intron
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GABBR2 | NM_005458.8 | c.2229+8C>T | splice_region_variant, intron_variant | ENST00000259455.4 | NP_005449.5 | |||
GABBR2 | XM_005252316.6 | c.1455+8C>T | splice_region_variant, intron_variant | XP_005252373.1 | ||||
GABBR2 | XM_017015331.3 | c.1935+8C>T | splice_region_variant, intron_variant | XP_016870820.1 | ||||
GABBR2 | XM_017015332.3 | c.1455+8C>T | splice_region_variant, intron_variant | XP_016870821.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GABBR2 | ENST00000259455.4 | c.2229+8C>T | splice_region_variant, intron_variant | 1 | NM_005458.8 | ENSP00000259455 | P1 | |||
GABBR2 | ENST00000634457.1 | c.456+8C>T | splice_region_variant, intron_variant | 5 | ENSP00000489352 | |||||
GABBR2 | ENST00000634354.1 | n.451+8C>T | splice_region_variant, intron_variant, non_coding_transcript_variant | 5 | ||||||
GABBR2 | ENST00000637410.1 | n.2007+8C>T | splice_region_variant, intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000443 AC: 11AN: 248054Hom.: 0 AF XY: 0.0000522 AC XY: 7AN XY: 134000
GnomAD4 exome AF: 0.0000275 AC: 40AN: 1452774Hom.: 0 Cov.: 31 AF XY: 0.0000304 AC XY: 22AN XY: 723162
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152318Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74482
ClinVar
Submissions by phenotype
Epileptic encephalopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at