5-180989061-C-G

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

Scores

18

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.381
Variant links:
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]

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BTNL3NM_197975.3 linkc.33C>G p.Phe11Leu missense_variant Exon 1 of 8 ENST00000342868.7 NP_932079.1 Q6UXE8-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BTNL3ENST00000342868.7 linkc.33C>G p.Phe11Leu missense_variant Exon 1 of 8 1 NM_197975.3 ENSP00000341787.6 Q6UXE8-1

Frequencies

GnomAD3 genomes
AF:
0.0202
AC:
2774
AN:
137558
Hom.:
375
Cov.:
24
show subpopulations
Gnomad AFR
AF:
0.0654
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00794
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000215
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0132
Gnomad NFE
AF:
0.000399
Gnomad OTH
AF:
0.0190
GnomAD3 exomes
AF:
0.00505
AC:
1048
AN:
207630
Hom.:
119
AF XY:
0.00356
AC XY:
401
AN XY:
112768
show subpopulations
Gnomad AFR exome
AF:
0.0634
Gnomad AMR exome
AF:
0.00355
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000143
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000331
Gnomad OTH exome
AF:
0.00242
GnomAD4 exome
AF:
0.00214
AC:
2804
AN:
1310436
Hom.:
429
Cov.:
30
AF XY:
0.00178
AC XY:
1164
AN XY:
652374
show subpopulations
Gnomad4 AFR exome
AF:
0.0669
Gnomad4 AMR exome
AF:
0.00417
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000967
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000208
Gnomad4 OTH exome
AF:
0.00465
GnomAD4 genome
AF:
0.0202
AC:
2780
AN:
137662
Hom.:
375
Cov.:
24
AF XY:
0.0188
AC XY:
1263
AN XY:
67078
show subpopulations
Gnomad4 AFR
AF:
0.0654
Gnomad4 AMR
AF:
0.00793
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000216
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000399
Gnomad4 OTH
AF:
0.0188
Alfa
AF:
0.0168
Hom.:
26
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.000519
AC:
2
ESP6500AA
AF:
0.0644
AC:
245
ESP6500EA
AF:
0.000264
AC:
2
ExAC
AF:
0.00596
AC:
665
Asia WGS
AF:
0.00241
AC:
8
AN:
3328

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

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.32
BayesDel_addAF
Benign
-0.61
T
BayesDel_noAF
Benign
-0.82
CADD
Benign
0.19
DANN
Benign
0.25
DEOGEN2
Benign
0.0019
T
Eigen
Benign
-1.6
Eigen_PC
Benign
-1.5
FATHMM_MKL
Benign
0.018
N
LIST_S2
Benign
0.34
T
MetaRNN
Benign
0.0026
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
-1.7
N
PrimateAI
Benign
0.39
T
PROVEAN
Benign
1.4
N
REVEL
Benign
0.028
Sift
Benign
1.0
T
Sift4G
Benign
1.0
T
Polyphen
0.0
B
Vest4
0.035
MutPred
0.40
Loss of helix (P = 0.1299);
MVP
0.24
MPC
0.46
ClinPred
0.0022
T
GERP RS
-0.27
Varity_R
0.039
gMVP
0.049

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs79915597; hg19: chr5-180416061; API