6-26459636-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007049.5(BTN2A1):c.238G>T(p.Gly80Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000088 in 1,614,144 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_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.238G>T | p.Gly80Cys | missense_variant | 3/8 | ENST00000312541.10 | |
BTN2A1 | NM_001197233.3 | c.55G>T | p.Gly19Cys | missense_variant | 2/7 | ||
BTN2A1 | NM_078476.4 | c.238G>T | p.Gly80Cys | missense_variant | 3/8 | ||
BTN2A1 | NM_001197234.3 | c.238G>T | p.Gly80Cys | missense_variant | 3/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BTN2A1 | ENST00000312541.10 | c.238G>T | p.Gly80Cys | missense_variant | 3/8 | 1 | NM_007049.5 | P1 | |
ENST00000707189.1 | n.1000-93551G>T | intron_variant, non_coding_transcript_variant | |||||||
ENST00000707191.1 | n.1001-73069G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000500 AC: 76AN: 152132Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000835 AC: 21AN: 251488Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135920
GnomAD4 exome AF: 0.0000451 AC: 66AN: 1461894Hom.: 0 Cov.: 32 AF XY: 0.0000440 AC XY: 32AN XY: 727248
GnomAD4 genome ? AF: 0.000499 AC: 76AN: 152250Hom.: 0 Cov.: 31 AF XY: 0.000524 AC XY: 39AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2021 | The c.238G>T (p.G80C) alteration is located in exon 3 (coding exon 2) of the BTN2A1 gene. This alteration results from a G to T substitution at nucleotide position 238, causing the glycine (G) at amino acid position 80 to be replaced by a cysteine (C). 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