rs9104
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_007047.5(BTN3A2):c.*2159G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,460 control chromosomes in the GnomAD database, including 2,042 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 0.16 ( 2036 hom., cov: 32)
Exomes 𝑓: 0.11 ( 6 hom. )
Consequence
BTN3A2
NM_007047.5 3_prime_UTR
NM_007047.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0160
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=-0.88).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BTN3A2 | NM_007047.5 | c.*2159G>A | 3_prime_UTR_variant | 11/11 | ENST00000377708.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BTN3A2 | ENST00000377708.7 | c.*2159G>A | 3_prime_UTR_variant | 11/11 | 1 | NM_007047.5 | P2 | ||
ENST00000707189.1 | n.1000-175266G>A | intron_variant, non_coding_transcript_variant | |||||||
ENST00000707191.1 | n.1001-154784G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.159 AC: 24096AN: 152012Hom.: 2037 Cov.: 32
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GnomAD4 exome AF: 0.114 AC: 38AN: 332Hom.: 6 Cov.: 0 AF XY: 0.118 AC XY: 20AN XY: 170
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GnomAD4 genome ? AF: 0.159 AC: 24115AN: 152128Hom.: 2036 Cov.: 32 AF XY: 0.157 AC XY: 11690AN XY: 74368
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at