Variant rs9268480 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001304561.2(BTNL2):c.1050G>A(p.Gln350Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 1,612,570 control chromosomes in the GnomAD database, including 62,843 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.24 ( 4552 hom., cov: 32)

Exomes 𝑓: 0.28 ( 58291 hom. )

Consequence

BTNL2
NM_001304561.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0350

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP7

Synonymous conserved (PhyloP=-0.035 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTNL2	NM_001304561.2 link	c.1050G>A	p.Gln350Gln	synonymous_variant	5/8	ENST00000454136.8	NP_001291490.1	Q9UIR0F8WBA1A0PJV4
TSBP1-AS1	NR_136245.1 link	n.303-9387C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTNL2	ENST00000454136.8 link	c.1050G>A	p.Gln350Gln	synonymous_variant	5/8	5	NM_001304561.2	ENSP00000390613.3		F8WBA1

Frequencies

GnomAD3 genomes

AF:

0.239

AC:

36297

AN:

152092

Hom.:

4553

Cov.:

show subpopulations

Gnomad AFR

AF:

0.180

Gnomad AMI

AF:

0.241

Gnomad AMR

AF:

0.294

Gnomad ASJ

AF:

0.304

Gnomad EAS

AF:

0.148

Gnomad SAS

AF:

0.231

Gnomad FIN

AF:

0.186

Gnomad MID

AF:

0.210

Gnomad NFE

AF:

0.275

Gnomad OTH

AF:

0.235

GnomAD3 exomes

AF:

0.258

AC:

63383

AN:

245970

Hom.:

8665

AF XY:

0.255

AC XY:

34227

AN XY:

134018

show subpopulations

Gnomad AFR exome

AF:

0.177

Gnomad AMR exome

AF:

0.341

Gnomad ASJ exome

AF:

0.295

Gnomad EAS exome

AF:

0.178

Gnomad SAS exome

AF:

0.214

Gnomad FIN exome

AF:

0.194

Gnomad NFE exome

AF:

0.276

Gnomad OTH exome

AF:

0.266

GnomAD4 exome

AF:

0.277

AC:

405220

AN:

1460360

Hom.:

58291

Cov.:

AF XY:

0.274

AC XY:

199227

AN XY:

726496

show subpopulations

Gnomad4 AFR exome

AF:

0.168

Gnomad4 AMR exome

AF:

0.338

Gnomad4 ASJ exome

AF:

0.296

Gnomad4 EAS exome

AF:

0.132

Gnomad4 SAS exome

AF:

0.216

Gnomad4 FIN exome

AF:

0.194

Gnomad4 NFE exome

AF:

0.293

Gnomad4 OTH exome

AF:

0.265

GnomAD4 genome

AF:

0.239

AC:

36310

AN:

152210

Hom.:

4552

Cov.:

AF XY:

0.235

AC XY:

17463

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.180

Gnomad4 AMR

AF:

0.294

Gnomad4 ASJ

AF:

0.304

Gnomad4 EAS

AF:

0.148

Gnomad4 SAS

AF:

0.231

Gnomad4 FIN

AF:

0.186

Gnomad4 NFE

AF:

0.275

Gnomad4 OTH

AF:

0.231

Alfa

AF:

0.262

Hom.:

3939

Bravo

AF:

0.252

Asia WGS

AF:

0.163

AC:

567

AN:

3478

EpiCase

AF:

0.275

EpiControl

AF:

0.274

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

2.9

DANN

Benign

0.70

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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