6-26368645-C-G
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_007047.5(BTN3A2):āc.166C>Gā(p.Pro56Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000133 in 1,613,934 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000013 ( 0 hom., cov: 31)
Exomes š: 0.00015 ( 0 hom. )
Consequence
BTN3A2
NM_007047.5 missense
NM_007047.5 missense
Scores
2
4
13
Clinical Significance
Conservation
PhyloP100: 1.46
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 Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.3340407).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BTN3A2 | NM_007047.5 | c.166C>G | p.Pro56Ala | missense_variant | 4/11 | ENST00000377708.7 | NP_008978.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BTN3A2 | ENST00000377708.7 | c.166C>G | p.Pro56Ala | missense_variant | 4/11 | 1 | NM_007047.5 | ENSP00000366937 | P2 | |
ENST00000707189.1 | n.1000-184542C>G | intron_variant, non_coding_transcript_variant | ||||||||
ENST00000707191.1 | n.1001-164060C>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152266Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000319 AC: 8AN: 251170Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135738
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GnomAD4 exome AF: 0.000146 AC: 213AN: 1461668Hom.: 0 Cov.: 31 AF XY: 0.000128 AC XY: 93AN XY: 727146
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152266Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74386
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 02, 2023 | The c.166C>G (p.P56A) alteration is located in exon 4 (coding exon 2) of the BTN3A2 gene. This alteration results from a C to G substitution at nucleotide position 166, causing the proline (P) at amino acid position 56 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
.;.;.;.;.;T;T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D;D;D;D;D;.;.;.;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
.;.;.;.;.;M;M;M;M
MutationTaster
Benign
N;N;N;N;N;N
PrimateAI
Benign
T
PROVEAN
Pathogenic
D;D;D;D;D;D;D;D;D
REVEL
Benign
Sift
Uncertain
D;D;D;D;D;D;D;D;D
Sift4G
Benign
T;T;T;D;D;T;T;T;T
Polyphen
1.0
.;.;.;.;.;D;D;D;D
Vest4
0.35, 0.34, 0.35, 0.35, 0.33, 0.35
MVP
MPC
3.3
ClinPred
D
GERP RS
Varity_R
gMVP
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