chr6-26463279-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.466C>T(p.His156Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,028 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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.466C>T | p.His156Tyr | missense_variant | 4/8 | ENST00000312541.10 | |
BTN2A1 | NM_001197233.3 | c.283C>T | p.His95Tyr | missense_variant | 3/7 | ||
BTN2A1 | NM_078476.4 | c.466C>T | p.His156Tyr | missense_variant | 4/8 | ||
BTN2A1 | NM_001197234.3 | c.466C>T | p.His156Tyr | missense_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BTN2A1 | ENST00000312541.10 | c.466C>T | p.His156Tyr | missense_variant | 4/8 | 1 | NM_007049.5 | P1 | |
ENST00000707189.1 | n.1000-89908C>T | intron_variant, non_coding_transcript_variant | |||||||
ENST00000707191.1 | n.1001-69426C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460028Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726306
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.466C>T (p.H156Y) alteration is located in exon 4 (coding exon 3) of the BTN2A1 gene. This alteration results from a C to T substitution at nucleotide position 466, causing the histidine (H) at amino acid position 156 to be replaced by a tyrosine (Y). 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