Variant 6-32396111-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001304561.2(BTNL2):c.1006G>A(p.Asp336Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0151 in 1,613,088 control chromosomes in the GnomAD database, including 1,128 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 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: 𝑓 0.012 ( 68 hom., cov: 32)

Exomes 𝑓: 0.015 ( 1060 hom. )

Consequence

BTNL2
NM_001304561.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.109

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]

BTNL2 links:

TSBP1-AS1 (HGNC:39756): (TSBP1 and BTNL2 antisense RNA 1)

TSBP1-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004987538).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTNL2	NM_001304561.2 linkuse as main transcript	c.1006G>A	p.Asp336Asn	missense_variant	5/8	ENST00000454136.8
TSBP1-AS1	NR_136245.1 linkuse as main transcript	n.303-9343C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTNL2	ENST00000454136.8 linkuse as main transcript	c.1006G>A	p.Asp336Asn	missense_variant	5/8	5	NM_001304561.2	P1
TSBP1-AS1	ENST00000645134.1 linkuse as main transcript	n.627+5358C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0122

AC:

1861

AN:

152196

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00227

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00929

Gnomad ASJ

AF:

0.0452

Gnomad EAS

AF:

0.109

Gnomad SAS

AF:

0.100

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00551

Gnomad OTH

AF:

0.0153

GnomAD3 exomes

AF:

0.0232

AC:

5725

AN:

246562

Hom.:

182

AF XY:

0.0263

AC XY:

3532

AN XY:

134366

show subpopulations

Gnomad AFR exome

AF:

0.00132

Gnomad AMR exome

AF:

0.00946

Gnomad ASJ exome

AF:

0.0498

Gnomad EAS exome

AF:

0.0824

Gnomad SAS exome

AF:

0.0817

Gnomad FIN exome

AF:

0.000231

Gnomad NFE exome

AF:

0.00685

Gnomad OTH exome

AF:

0.0216

GnomAD4 exome

AF:

0.0155

AC:

22571

AN:

1460774

Hom.:

1060

Cov.:

AF XY:

0.0179

AC XY:

12998

AN XY:

726708

show subpopulations

Gnomad4 AFR exome

AF:

0.00146

Gnomad4 AMR exome

AF:

0.00993

Gnomad4 ASJ exome

AF:

0.0489

Gnomad4 EAS exome

AF:

0.162

Gnomad4 SAS exome

AF:

0.0828

Gnomad4 FIN exome

AF:

0.000268

Gnomad4 NFE exome

AF:

0.00524

Gnomad4 OTH exome

AF:

0.0195

GnomAD4 genome

AF:

0.0122

AC:

1859

AN:

152314

Hom.:

Cov.:

AF XY:

0.0142

AC XY:

1056

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.00226

Gnomad4 AMR

AF:

0.00928

Gnomad4 ASJ

AF:

0.0452

Gnomad4 EAS

AF:

0.109

Gnomad4 SAS

AF:

0.100

Gnomad4 FIN

AF:

0.000377

Gnomad4 NFE

AF:

0.00551

Gnomad4 OTH

AF:

0.0147

Alfa

AF:

0.00979

Hom.:

Bravo

AF:

0.00990

TwinsUK

AF:

0.00539

AC:

ALSPAC

AF:

0.00415

AC:

ESP6500AA

AF:

0.00132

AC:

ESP6500EA

AF:

0.00904

AC:

ExAC

AF:

0.0237

AC:

2811

Asia WGS

AF:

0.0810

AC:

282

AN:

3478

EpiCase

AF:

0.00796

EpiControl

AF:

0.00699

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.087

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.46

CADD

Benign

DANN

Benign

0.67

DEOGEN2

Benign

0.0064

T;T;.

Eigen

Benign

-0.67

Eigen_PC

Benign

-0.59

FATHMM_MKL

Benign

0.054

MetaRNN

Benign

0.0050

T;T;T

MetaSVM

Benign

-1.1

MutationTaster

Benign

1.0

N;N;N;N;N;N;N

PrimateAI

Uncertain

0.49

Sift4G

Benign

0.33

T;T;T

Polyphen

0.092

.;B;.

Vest4

0.020

MPC

0.41

ClinPred

0.0072

GERP RS

2.3

Varity_R

0.094

gMVP

0.32

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

LitVar

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over