5-180989061-C-G
Variant names:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_197975.3(BTNL3):c.33C>G(p.Phe11Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00386 in 1,448,098 control chromosomes in the GnomAD database, including 804 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.020 ( 375 hom., cov: 24)
Exomes 𝑓: 0.0021 ( 429 hom. )
Consequence
BTNL3
NM_197975.3 missense
NM_197975.3 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: -0.381
Genes affected
BTNL3 (HGNC:1143): (butyrophilin like 3) Predicted to enable signaling receptor binding activity. Predicted to be involved in T cell receptor signaling pathway and regulation of cytokine production. Predicted to be integral component of membrane. Predicted to be active in external side of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=0.0025765002).
BP6
Variant 5-180989061-C-G is Benign according to our data. Variant chr5-180989061-C-G is described in ClinVar as [Benign]. Clinvar id is 781740.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0633 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0202 AC: 2774AN: 137558Hom.: 375 Cov.: 24
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GnomAD3 exomes AF: 0.00505 AC: 1048AN: 207630Hom.: 119 AF XY: 0.00356 AC XY: 401AN XY: 112768
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GnomAD4 exome AF: 0.00214 AC: 2804AN: 1310436Hom.: 429 Cov.: 30 AF XY: 0.00178 AC XY: 1164AN XY: 652374
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GnomAD4 genome AF: 0.0202 AC: 2780AN: 137662Hom.: 375 Cov.: 24 AF XY: 0.0188 AC XY: 1263AN XY: 67078
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jun 22, 2017
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Loss of helix (P = 0.1299);
MVP
MPC
ClinPred
T
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