rs17202456
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001304561.2(BTNL2):c.1078+42C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 1,469,812 control chromosomes in the GnomAD database, including 15,162 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 0.14 ( 1609 hom., cov: 32)
Exomes 𝑓: 0.14 ( 13553 hom. )
Consequence
BTNL2
NM_001304561.2 intron
NM_001304561.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.341
Genes affected
BTNL2 (HGNC:1142): (butyrophilin like 2) This gene encodes a major histocompatibility complex, class II associated, type I transmembrane protein which belongs to the butyrophilin-like B7 family of immunoregulators. It is thought to be involved in immune surveillance, serving as a negative T-cell regulator by decreasing T-cell proliferation and cytokine release. The encoded protein contains an N-terminal signal peptide, two pairs of immunoglobulin-like domains, separated by a heptad peptide sequence, and a C-terminal transmembrane domain. Naturally occurring mutations in this gene are associated with sarcoidosis, rheumatoid arthritis, ulcerative colitis, inflammatory bowel disease, myositis, type 1 diabetes, systemic lupus erythematosus, acute coronary syndrome, and prostate cancer. [provided by RefSeq, May 2017]
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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=-0.84).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BTNL2 | NM_001304561.2 | c.1078+42C>T | intron_variant | ENST00000454136.8 | |||
TSBP1-AS1 | NR_136245.1 | n.303-9457G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BTNL2 | ENST00000454136.8 | c.1078+42C>T | intron_variant | 5 | NM_001304561.2 | P1 | |||
TSBP1-AS1 | ENST00000645134.1 | n.627+5244G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.139 AC: 21203AN: 152078Hom.: 1609 Cov.: 32
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GnomAD3 exomes AF: 0.134 AC: 27924AN: 208808Hom.: 2200 AF XY: 0.132 AC XY: 14843AN XY: 112764
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GnomAD4 exome AF: 0.138 AC: 181768AN: 1317616Hom.: 13553 Cov.: 20 AF XY: 0.136 AC XY: 88587AN XY: 652094
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GnomAD4 genome ? AF: 0.139 AC: 21206AN: 152196Hom.: 1609 Cov.: 32 AF XY: 0.143 AC XY: 10629AN XY: 74404
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ClinVar
Not reported inComputational scores
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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