Variant 6-32403192-TG-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001304561.2(BTNL2):c.451del(p.His151ThrfsTer96) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0803 in 1,606,212 control chromosomes in the GnomAD database, including 6,764 homozygotes. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.10 ( 948 hom., cov: 30)

Exomes 𝑓: 0.078 ( 5816 hom. )

Consequence

BTNL2
NM_001304561.2 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.35

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 6-32403192-TG-T is Benign according to our data. Variant chr6-32403192-TG-T is described in ClinVar as [Benign]. Clinvar id is 1271189.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 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.451del	p.His151ThrfsTer96	frameshift_variant	3/8	ENST00000454136.8
TSBP1-AS1	NR_136245.1 linkuse as main transcript	n.303-2260del		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.451del	p.His151ThrfsTer96	frameshift_variant	3/8	5	NM_001304561.2	P1
TSBP1-AS1	ENST00000645134.1 linkuse as main transcript	n.628-475del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15810

AN:

151922

Hom.:

946

Cov.:

show subpopulations

Gnomad AFR

AF:

0.119

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.132

Gnomad ASJ

AF:

0.0334

Gnomad EAS

AF:

0.198

Gnomad SAS

AF:

0.0934

Gnomad FIN

AF:

0.174

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.0759

Gnomad OTH

AF:

0.114

GnomAD3 exomes

AF:

0.108

AC:

25825

AN:

238974

Hom.:

1853

AF XY:

0.103

AC XY:

13383

AN XY:

130456

show subpopulations

Gnomad AFR exome

AF:

0.115

Gnomad AMR exome

AF:

0.190

Gnomad ASJ exome

AF:

0.0334

Gnomad EAS exome

AF:

0.194

Gnomad SAS exome

AF:

0.0843

Gnomad FIN exome

AF:

0.165

Gnomad NFE exome

AF:

0.0703

Gnomad OTH exome

AF:

0.0987

GnomAD4 exome

AF:

0.0778

AC:

113143

AN:

1454172

Hom.:

5816

Cov.:

AF XY:

0.0777

AC XY:

56226

AN XY:

723280

show subpopulations

Gnomad4 AFR exome

AF:

0.122

Gnomad4 AMR exome

AF:

0.183

Gnomad4 ASJ exome

AF:

0.0349

Gnomad4 EAS exome

AF:

0.188

Gnomad4 SAS exome

AF:

0.0842

Gnomad4 FIN exome

AF:

0.168

Gnomad4 NFE exome

AF:

0.0644

Gnomad4 OTH exome

AF:

0.0854

GnomAD4 genome

AF:

0.104

AC:

15820

AN:

152040

Hom.:

948

Cov.:

AF XY:

0.108

AC XY:

8054

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.119

Gnomad4 AMR

AF:

0.132

Gnomad4 ASJ

AF:

0.0334

Gnomad4 EAS

AF:

0.197

Gnomad4 SAS

AF:

0.0927

Gnomad4 FIN

AF:

0.174

Gnomad4 NFE

AF:

0.0758

Gnomad4 OTH

AF:

0.113

Alfa

AF:

0.0838

Hom.:

101

Bravo

AF:

0.102

Asia WGS

AF:

0.139

AC:

484

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 15, 2020

This variant is associated with the following publications: (PMID: 31956453, 22829467) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.17

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over