rs12176317
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_007047.5(BTN3A2):c.716-339A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0829 in 255,654 control chromosomes in the GnomAD database, including 1,101 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.076 ( 555 hom., cov: 32)
Exomes 𝑓: 0.093 ( 546 hom. )
Consequence
BTN3A2
NM_007047.5 intron
NM_007047.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0630
Genes affected
BTN3A2 (HGNC:1139): (butyrophilin subfamily 3 member A2) This gene encodes a member of the immunoglobulin superfamily, which resides in the juxta-telomeric region of the major histocompatability class 1 locus and is clustered with the other family members on chromosome 6. The encoded protein may be involved in the adaptive immune response. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BTN3A2 | NM_007047.5 | c.716-339A>G | intron_variant | ENST00000377708.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BTN3A2 | ENST00000377708.7 | c.716-339A>G | intron_variant | 1 | NM_007047.5 | P2 | |||
ENST00000707189.1 | n.1000-180629A>G | intron_variant, non_coding_transcript_variant | |||||||
ENST00000707191.1 | n.1001-160147A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0764 AC: 11621AN: 152156Hom.: 556 Cov.: 32
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GnomAD4 exome AF: 0.0927 AC: 9587AN: 103380Hom.: 546 AF XY: 0.0931 AC XY: 5060AN XY: 54322
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GnomAD4 genome ? AF: 0.0763 AC: 11612AN: 152274Hom.: 555 Cov.: 32 AF XY: 0.0732 AC XY: 5453AN XY: 74466
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at