6-32399482-T-G

Variant names:

• chr6-32399482-T-G
• rs2294884
• NM_001304561.2:c.730+2303A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001304561.2(BTNL2):​c.730+2303A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,132 control chromosomes in the GnomAD database, including 2,691 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 0.18 (2691 hom., cov: 32)
• Consequence: BTNL2 NM_001304561.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 33 publications found

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]

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001304561.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTNL2	NM_001304561.2	MANE Select	c.730+2303A>C		intron	N/A	NP_001291490.1
	TSBP1-AS1	NR_136245.1		n.303-5972T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTNL2	ENST00000454136.8	TSL:5 MANE Select	c.730+2303A>C		intron	N/A	ENSP00000390613.3
	BTNL2	ENST00000465865.6	TSL:1	n.*5+2303A>C		intron	N/A	ENSP00000420063.1
	BTNL2	ENST00000544175.3	TSL:1	n.207+2303A>C		intron	N/A	ENSP00000443364.2

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27051 AN: 152014 Hom.: 2688 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.0550

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.176

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.178 AC: 27063 AN: 152132 Hom.: 2691 Cov.: 32 AF XY: 0.186 AC XY: 13820 AN XY: 74376

African (AFR) AF: 0.139 AC: 5780 AN: 41526

American (AMR) AF: 0.189 AC: 2892 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0550 AC: 191 AN: 3472

East Asian (EAS) AF: 0.215 AC: 1113 AN: 5176

South Asian (SAS) AF: 0.127 AC: 612 AN: 4818

European-Finnish (FIN) AF: 0.377 AC: 3975 AN: 10554

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11870 AN: 67978

Other (OTH) AF: 0.174 AC: 368 AN: 2110

Alfa AF: 0.167 Hom.: 6159

Bravo AF: 0.162

Asia WGS AF: 0.171 AC: 592 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.62
PhyloP100		-0.097
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2294884; hg19: chr6-32367259;