chr10-102358157-A-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_001377137.1(GBF1):āc.758A>Gā(p.Asn253Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000121 in 1,613,750 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Uncertain significance (ā ).
Frequency
Consequence
NM_001377137.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GBF1 | NM_001377137.1 | c.758A>G | p.Asn253Ser | missense_variant | 9/40 | ENST00000369983.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GBF1 | ENST00000369983.5 | c.758A>G | p.Asn253Ser | missense_variant | 9/40 | 1 | NM_001377137.1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 151984Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000167 AC: 42AN: 251352Hom.: 1 AF XY: 0.000206 AC XY: 28AN XY: 135848
GnomAD4 exome AF: 0.000121 AC: 177AN: 1461648Hom.: 1 Cov.: 30 AF XY: 0.000147 AC XY: 107AN XY: 727160
GnomAD4 genome AF: 0.000118 AC: 18AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 13, 2024 | The c.758A>G (p.N253S) alteration is located in exon 9 (coding exon 8) of the GBF1 gene. This alteration results from a A to G substitution at nucleotide position 758, causing the asparagine (N) at amino acid position 253 to be replaced by a serine (S). 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