chr6-26458667-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.31C>T(p.Arg11Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,613,956 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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.31C>T | p.Arg11Trp | missense_variant | 2/8 | ENST00000312541.10 | |
BTN2A1 | NM_078476.4 | c.31C>T | p.Arg11Trp | missense_variant | 2/8 | ||
BTN2A1 | NM_001197234.3 | c.31C>T | p.Arg11Trp | missense_variant | 2/8 | ||
BTN2A1 | NM_001197233.3 | c.-102+525C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BTN2A1 | ENST00000312541.10 | c.31C>T | p.Arg11Trp | missense_variant | 2/8 | 1 | NM_007049.5 | P1 | |
ENST00000707189.1 | n.1000-94520C>T | intron_variant, non_coding_transcript_variant | |||||||
ENST00000707191.1 | n.1001-74038C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000111 AC: 28AN: 251466Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135908
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461866Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 727236
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152090Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 09, 2022 | The c.31C>T (p.R11W) alteration is located in exon 2 (coding exon 1) of the BTN2A1 gene. This alteration results from a C to T substitution at nucleotide position 31, causing the arginine (R) at amino acid position 11 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