rs2076030
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_027795.1(BTN2A3P):n.1452+105G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0912 in 711,296 control chromosomes in the GnomAD database, including 3,620 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 0.077 ( 558 hom., cov: 31)
Exomes 𝑓: 0.095 ( 3062 hom. )
Consequence
BTN2A3P
NR_027795.1 intron, non_coding_transcript
NR_027795.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.226
Genes affected
BTN2A3P (HGNC:13229): (butyrophilin subfamily 2 member A3, pseudogene) The butyrophilin (BTN) genes are a group of major histocompatibility complex (MHC)-associated genes that encode type I membrane proteins with 2 extracellular immunoglobulin (Ig) domains and an intracellular B30.2 (PRYSPRY) domain. Three subfamilies of human BTN genes are located in the MHC class I region: the single-copy BTN1A1 gene (MIM 601610) and the BTN2 (e.g., BTN2A3) and BTN3 (e.g., BNT3A1; MIM 613593) genes, which have undergone tandem duplication, resulting in 3 copies of each (summary by Smith et al., 2010 [PubMed 20208008]).[supplied by OMIM, Nov 2010]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BTN2A3P | NR_027795.1 | n.1452+105G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BTN2A3P | ENST00000377662.6 | n.706+105G>A | intron_variant, non_coding_transcript_variant | ||||||
BTN2A3P | ENST00000686357.1 | n.1367+105G>A | intron_variant, non_coding_transcript_variant | ||||||
ENST00000707189.1 | n.1000-126559G>A | intron_variant, non_coding_transcript_variant | |||||||
ENST00000707191.1 | n.1001-106077G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0768 AC: 11674AN: 152074Hom.: 559 Cov.: 31
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GnomAD4 exome AF: 0.0952 AC: 53236AN: 559104Hom.: 3062 AF XY: 0.0959 AC XY: 28507AN XY: 297220
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GnomAD4 genome ? AF: 0.0767 AC: 11667AN: 152192Hom.: 558 Cov.: 31 AF XY: 0.0740 AC XY: 5509AN XY: 74412
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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