X-154712546-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001081573.3(GAB3):c.752C>T(p.Ser251Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000144 in 1,184,514 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. 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 Uncertain significance (★).
Frequency
Consequence
NM_001081573.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GAB3 | NM_001081573.3 | c.752C>T | p.Ser251Leu | missense_variant | 4/10 | ENST00000424127.3 | NP_001075042.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GAB3 | ENST00000424127.3 | c.752C>T | p.Ser251Leu | missense_variant | 4/10 | 1 | NM_001081573.3 | ENSP00000399588 | A2 | |
GAB3 | ENST00000369575.7 | c.749C>T | p.Ser250Leu | missense_variant | 4/10 | 1 | ENSP00000358588 | P4 | ||
GAB3 | ENST00000496390.5 | n.616+661C>T | intron_variant, non_coding_transcript_variant | 1 | ||||||
GAB3 | ENST00000369568.8 | c.752C>T | p.Ser251Leu | missense_variant | 4/9 | 2 | ENSP00000358581 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000179 AC: 2AN: 111725Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33939
GnomAD3 exomes AF: 0.0000384 AC: 6AN: 156437Hom.: 0 AF XY: 0.0000401 AC XY: 2AN XY: 49925
GnomAD4 exome AF: 0.0000140 AC: 15AN: 1072789Hom.: 0 Cov.: 30 AF XY: 0.0000173 AC XY: 6AN XY: 347043
GnomAD4 genome AF: 0.0000179 AC: 2AN: 111725Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33939
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 04, 2023 | The c.752C>T (p.S251L) alteration is located in exon 4 (coding exon 4) of the GAB3 gene. This alteration results from a C to T substitution at nucleotide position 752, causing the serine (S) at amino acid position 251 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at