rs2072803
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006995.5(BTN2A2):c.980-88G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 1,601,016 control chromosomes in the GnomAD database, including 11,142 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.078 ( 585 hom., cov: 32)
Exomes 𝑓: 0.12 ( 10557 hom. )
Consequence
BTN2A2
NM_006995.5 intron
NM_006995.5 intron
Scores
1
12
Clinical Significance
Conservation
PhyloP100: 0.580
Genes affected
BTN2A2 (HGNC:1137): (butyrophilin subfamily 2 member A2) Butyrophilin is the major protein associated with fat droplets in the milk. This gene is a member of the BTN2 subfamily of genes, which encode proteins belonging to the butyrophilin protein family. The gene is located in a cluster on chromosome 6, consisting of seven genes belonging to the expanding B7/butyrophilin-like group, a subset of the immunoglobulin gene superfamily. The encoded protein is a type I receptor glycoprotein involved in lipid, fatty-acid and sterol metabolism. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0015104413).
BP6
?
Variant 6-26392287-G-C is Benign according to our data. Variant chr6-26392287-G-C is described in ClinVar as [Benign]. Clinvar id is 3059309.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BTN2A2 | NM_006995.5 | c.980-88G>C | intron_variant | ENST00000356709.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BTN2A2 | ENST00000356709.9 | c.980-88G>C | intron_variant | 1 | NM_006995.5 | P1 | |||
ENST00000707189.1 | n.1000-160900G>C | intron_variant, non_coding_transcript_variant | |||||||
ENST00000707191.1 | n.1001-140418G>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0785 AC: 11948AN: 152140Hom.: 587 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0855 AC: 19218AN: 224716Hom.: 963 AF XY: 0.0885 AC XY: 10788AN XY: 121840
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GnomAD4 exome AF: 0.115 AC: 166972AN: 1448758Hom.: 10557 Cov.: 30 AF XY: 0.114 AC XY: 82158AN XY: 719436
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GnomAD4 genome ? AF: 0.0784 AC: 11939AN: 152258Hom.: 585 Cov.: 32 AF XY: 0.0757 AC XY: 5632AN XY: 74442
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
BTN2A2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 04, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P;P;P;P
PROVEAN
Benign
N
REVEL
Benign
Sift
Pathogenic
D
Vest4
ClinPred
T
GERP RS
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at