Variant chr6-32394044-C-T 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.1374G>A(p.Thr458=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 1,549,740 control chromosomes in the GnomAD database, including 18,055 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 0.12 ( 1292 hom., cov: 32)

Exomes 𝑓: 0.14 ( 16763 hom. )

Consequence

BTNL2
NM_001304561.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.546

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=-0.75).

BP7

Synonymous conserved (PhyloP=0.546 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.151 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.1374G>A	p.Thr458=	synonymous_variant	7/8	ENST00000454136.8
TSBP1-AS1	NR_136245.1 linkuse as main transcript	n.303-11410C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
BTNL2	ENST00000454136.8 linkuse as main transcript	c.1374G>A	p.Thr458=	synonymous_variant	7/8	5	NM_001304561.2	P1
TSBP1-AS1	ENST00000645134.1 linkuse as main transcript	n.627+3291C>T		intron_variant, non_coding_transcript_variant
TSBP1-AS1	ENST00000642577.1 linkuse as main transcript	n.708+3291C>T		intron_variant, non_coding_transcript_variant
TSBP1-AS1	ENST00000645167.1 linkuse as main transcript	n.124-12073C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.124

AC:

18876

AN:

152068

Hom.:

1293

Cov.:

show subpopulations

Gnomad AFR

AF:

0.117

Gnomad AMI

AF:

0.120

Gnomad AMR

AF:

0.0732

Gnomad ASJ

AF:

0.0949

Gnomad EAS

AF:

0.0435

Gnomad SAS

AF:

0.0195

Gnomad FIN

AF:

0.141

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.154

Gnomad OTH

AF:

0.106

GnomAD3 exomes

AF:

0.101

AC:

14956

AN:

148536

Hom.:

1082

AF XY:

0.0977

AC XY:

7823

AN XY:

80050

show subpopulations

Gnomad AFR exome

AF:

0.119

Gnomad AMR exome

AF:

0.0619

Gnomad ASJ exome

AF:

0.0897

Gnomad EAS exome

AF:

0.0563

Gnomad SAS exome

AF:

0.0187

Gnomad FIN exome

AF:

0.134

Gnomad NFE exome

AF:

0.149

Gnomad OTH exome

AF:

0.102

GnomAD4 exome

AF:

0.145

AC:

202422

AN:

1397554

Hom.:

16763

Cov.:

AF XY:

0.141

AC XY:

96868

AN XY:

689340

show subpopulations

Gnomad4 AFR exome

AF:

0.116

Gnomad4 AMR exome

AF:

0.0650

Gnomad4 ASJ exome

AF:

0.0948

Gnomad4 EAS exome

AF:

0.0402

Gnomad4 SAS exome

AF:

0.0192

Gnomad4 FIN exome

AF:

0.139

Gnomad4 NFE exome

AF:

0.164

Gnomad4 OTH exome

AF:

0.131

GnomAD4 genome

AF:

0.124

AC:

18884

AN:

152186

Hom.:

1292

Cov.:

AF XY:

0.118

AC XY:

8764

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.116

Gnomad4 AMR

AF:

0.0731

Gnomad4 ASJ

AF:

0.0949

Gnomad4 EAS

AF:

0.0436

Gnomad4 SAS

AF:

0.0195

Gnomad4 FIN

AF:

0.141

Gnomad4 NFE

AF:

0.154

Gnomad4 OTH

AF:

0.105

Alfa

AF:

0.130

Hom.:

1787

Bravo

AF:

0.119

Asia WGS

AF:

0.0490

AC:

170

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

2.8

DANN

Benign

0.52

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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