chr11-66338273-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015399.4(BRMS1):c.703G>A(p.Ala235Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000103 in 1,610,214 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015399.4 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 |
---|---|---|---|---|---|---|---|
BRMS1 | NM_015399.4 | c.703G>A | p.Ala235Thr | missense_variant | 9/10 | ENST00000359957.8 | |
BRMS1 | NM_001024957.2 | c.703G>A | p.Ala235Thr | missense_variant | 9/10 | ||
BRMS1 | XM_024448425.2 | c.694-384G>A | intron_variant | ||||
BRMS1 | XM_024448426.2 | c.693+448G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRMS1 | ENST00000359957.8 | c.703G>A | p.Ala235Thr | missense_variant | 9/10 | 1 | NM_015399.4 | P1 | |
ENST00000526655.1 | n.424-1510C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152274Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000124 AC: 30AN: 242342Hom.: 0 AF XY: 0.000107 AC XY: 14AN XY: 130958
GnomAD4 exome AF: 0.000103 AC: 150AN: 1457940Hom.: 0 Cov.: 31 AF XY: 0.0000869 AC XY: 63AN XY: 724788
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152274Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74402
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 11, 2022 | The c.703G>A (p.A235T) alteration is located in exon 9 (coding exon 8) of the BRMS1 gene. This alteration results from a G to A substitution at nucleotide position 703, causing the alanine (A) at amino acid position 235 to be replaced by a threonine (T). 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