chr1-190160868-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_199051.3(BRINP3):c.984A>T(p.Lys328Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000345 in 1,451,036 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_199051.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRINP3 | NM_199051.3 | c.984A>T | p.Lys328Asn | missense_variant | 7/8 | ENST00000367462.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRINP3 | ENST00000367462.5 | c.984A>T | p.Lys328Asn | missense_variant | 7/8 | 1 | NM_199051.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000837 AC: 2AN: 238944Hom.: 0 AF XY: 0.00000775 AC XY: 1AN XY: 129074
GnomAD4 exome AF: 0.00000345 AC: 5AN: 1451036Hom.: 0 Cov.: 30 AF XY: 0.00000277 AC XY: 2AN XY: 721318
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 22, 2024 | The c.984A>T (p.K328N) alteration is located in exon 7 (coding exon 6) of the BRINP3 gene. This alteration results from a A to T substitution at nucleotide position 984, causing the lysine (K) at amino acid position 328 to be replaced by an asparagine (N). 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