chr1-190098328-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_199051.3(BRINP3):c.1991A>G(p.Asn664Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,614,206 control chromosomes in the GnomAD database, including 2 homozygotes. 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRINP3 | NM_199051.3 | c.1991A>G | p.Asn664Ser | missense_variant | 8/8 | ENST00000367462.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRINP3 | ENST00000367462.5 | c.1991A>G | p.Asn664Ser | missense_variant | 8/8 | 1 | NM_199051.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000434 AC: 66AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000262 AC: 66AN: 251476Hom.: 1 AF XY: 0.000213 AC XY: 29AN XY: 135906
GnomAD4 exome AF: 0.0000725 AC: 106AN: 1461892Hom.: 2 Cov.: 31 AF XY: 0.0000743 AC XY: 54AN XY: 727246
GnomAD4 genome ? AF: 0.000433 AC: 66AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.000510 AC XY: 38AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 22, 2021 | The c.1991A>G (p.N664S) alteration is located in exon 8 (coding exon 7) of the BRINP3 gene. This alteration results from a A to G substitution at nucleotide position 1991, causing the asparagine (N) at amino acid position 664 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