GeneBe

rs41441651

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4

The NM_001304561.2(BTNL2):​c.1006G>C​(p.Asp336His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

BTNL2
NM_001304561.2 missense

Scores

4
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.109

Publications

22 publications found
Variant links:
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]
TSBP1-AS1 (HGNC:39756): (TSBP1 and BTNL2 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.40061626).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001304561.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
BTNL2
NM_001304561.2
MANE Select
c.1006G>Cp.Asp336His
missense
Exon 5 of 8NP_001291490.1Q9UIR0-7
TSBP1-AS1
NR_136245.1
n.303-9343C>G
intron
N/A

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
BTNL2
ENST00000454136.8
TSL:5 MANE Select
c.1006G>Cp.Asp336His
missense
Exon 5 of 8ENSP00000390613.3Q9UIR0-7
BTNL2
ENST00000465865.6
TSL:1
n.*281G>C
non_coding_transcript_exon
Exon 4 of 5ENSP00000420063.1F8WDK6
BTNL2
ENST00000544175.3
TSL:1
n.*267G>C
non_coding_transcript_exon
Exon 4 of 5ENSP00000443364.2Q9UIR0-8

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
56
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
60
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.19
BayesDel_addAF
Benign
-0.019
T
BayesDel_noAF
Benign
-0.27
CADD
Benign
19
DANN
Uncertain
0.99
DEOGEN2
Benign
0.024
T
Eigen
Benign
0.054
Eigen_PC
Benign
-0.092
FATHMM_MKL
Benign
0.12
N
M_CAP
Benign
0.021
T
MetaRNN
Benign
0.40
T
MetaSVM
Benign
-0.92
T
MutationAssessor
Uncertain
2.1
M
PhyloP100
-0.11
PrimateAI
Uncertain
0.49
T
PROVEAN
Benign
-1.5
N
REVEL
Benign
0.16
Sift
Benign
0.055
T
Sift4G
Uncertain
0.0080
D
Polyphen
1.0
D
Vest4
0.10
MutPred
0.33
Gain of catalytic residue at D336 (P = 0.0876)
MVP
0.80
MPC
1.2
ClinPred
0.78
D
GERP RS
2.3
Varity_R
0.13
gMVP
0.56
Mutation Taster
=95/5
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs41441651; hg19: chr6-32363888; API