chr6-26465331-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007049.5(BTN2A1):c.859C>T(p.Arg287Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,613,928 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007049.5 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 |
---|---|---|---|---|---|---|---|
BTN2A1 | NM_007049.5 | c.859C>T | p.Arg287Trp | missense_variant | 5/8 | ENST00000312541.10 | |
BTN2A1 | NM_001197233.3 | c.676C>T | p.Arg226Trp | missense_variant | 4/7 | ||
BTN2A1 | NM_078476.4 | c.859C>T | p.Arg287Trp | missense_variant | 5/8 | ||
BTN2A1 | NM_001197234.3 | c.859C>T | p.Arg287Trp | missense_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BTN2A1 | ENST00000312541.10 | c.859C>T | p.Arg287Trp | missense_variant | 5/8 | 1 | NM_007049.5 | P1 | |
ENST00000707189.1 | n.1000-87856C>T | intron_variant, non_coding_transcript_variant | |||||||
ENST00000707191.1 | n.1001-67374C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 151922Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251448Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135884
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461888Hom.: 1 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 727242
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152040Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 08, 2024 | The c.859C>T (p.R287W) alteration is located in exon 5 (coding exon 4) of the BTN2A1 gene. This alteration results from a C to T substitution at nucleotide position 859, causing the arginine (R) at amino acid position 287 to be replaced by a tryptophan (W). 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