chr17-60924424-T-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting
The NM_017679.5(BCAS3):c.1011T>G(p.Asp337Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00012 in 1,613,914 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017679.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCAS3 | NM_017679.5 | c.1011T>G | p.Asp337Glu | missense_variant | 13/24 | ENST00000407086.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCAS3 | ENST00000407086.8 | c.1011T>G | p.Asp337Glu | missense_variant | 13/24 | 1 | NM_017679.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000481 AC: 12AN: 249570Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135400
GnomAD4 exome AF: 0.000123 AC: 180AN: 1461660Hom.: 0 Cov.: 31 AF XY: 0.0000990 AC XY: 72AN XY: 727136
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74458
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 13, 2024 | The c.1011T>G (p.D337E) alteration is located in exon 13 (coding exon 12) of the BCAS3 gene. This alteration results from a T to G substitution at nucleotide position 1011, causing the aspartic acid (D) at amino acid position 337 to be replaced by a glutamic acid (E). 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