6-26413612-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007048.6(BTN3A1):c.1462G>A(p.Val488Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000144 in 1,613,990 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_007048.6 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 |
---|---|---|---|---|---|---|---|
BTN3A1 | NM_007048.6 | c.1462G>A | p.Val488Ile | missense_variant | 10/10 | ENST00000289361.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BTN3A1 | ENST00000289361.11 | c.1462G>A | p.Val488Ile | missense_variant | 10/10 | 1 | NM_007048.6 | P1 | |
ENST00000707189.1 | n.1000-139575G>A | intron_variant, non_coding_transcript_variant | |||||||
ENST00000707191.1 | n.1001-119093G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000139 AC: 35AN: 251424Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135880
GnomAD4 exome AF: 0.000148 AC: 216AN: 1461884Hom.: 0 Cov.: 32 AF XY: 0.000147 AC XY: 107AN XY: 727244
GnomAD4 genome AF: 0.000112 AC: 17AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2023 | The c.1462G>A (p.V488I) alteration is located in exon 10 (coding exon 9) of the BTN3A1 gene. This alteration results from a G to A substitution at nucleotide position 1462, causing the valine (V) at amino acid position 488 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