chr6-26463464-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007049.5(BTN2A1):c.651G>A(p.Met217Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,614,162 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.651G>A | p.Met217Ile | missense_variant | 4/8 | ENST00000312541.10 | |
BTN2A1 | NM_001197233.3 | c.468G>A | p.Met156Ile | missense_variant | 3/7 | ||
BTN2A1 | NM_078476.4 | c.651G>A | p.Met217Ile | missense_variant | 4/8 | ||
BTN2A1 | NM_001197234.3 | c.651G>A | p.Met217Ile | missense_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BTN2A1 | ENST00000312541.10 | c.651G>A | p.Met217Ile | missense_variant | 4/8 | 1 | NM_007049.5 | P1 | |
ENST00000707189.1 | n.1000-89723G>A | intron_variant, non_coding_transcript_variant | |||||||
ENST00000707191.1 | n.1001-69241G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152164Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251452Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135888
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461880Hom.: 0 Cov.: 31 AF XY: 0.0000330 AC XY: 24AN XY: 727242
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152282Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2022 | The c.651G>A (p.M217I) alteration is located in exon 4 (coding exon 3) of the BTN2A1 gene. This alteration results from a G to A substitution at nucleotide position 651, causing the methionine (M) at amino acid position 217 to be replaced by an isoleucine (I). 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