rs3799380

chr6-26466954-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007049.5(BTN2A1):c.982+866T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,156 control chromosomes in the GnomAD database, including 9,608 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 0.30 (9608 hom., cov: 32)
• Consequence: BTN2A1 NM_007049.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

Genes affected

BTN2A1 (HGNC:1136): (butyrophilin subfamily 2 member A1) This gene encodes a member of the immunoglobulin superfamily. The gene is located in a cluster of butyrophilin-like genes in the juxta-telomeric region of the major histocompatibility complex on chromosome 6. A pseudogene of this gene has been identified in this cluster. The encoded protein is an integral plasma membrane protein involved in lipid, fatty-acid, and sterol metabolism. Alterations in this gene may be associated with several disease states including metabolic syndrome. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2013]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTN2A1	NM_007049.5	c.982+866T>C		intron_variant		ENST00000312541.10
BTN2A1	NM_001197233.3	c.799+866T>C		intron_variant
BTN2A1	NM_001197234.3	c.982+866T>C		intron_variant
BTN2A1	NM_078476.4	c.983-765T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTN2A1	ENST00000312541.10	c.982+866T>C		intron_variant		1	NM_007049.5	P1
	ENST00000707189.1	n.1000-86233T>C		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1001-65751T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45664 AN: 152038 Hom.: 9577 Cov.: 32

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.301 AC: 45741 AN: 152156 Hom.: 9608 Cov.: 32 AF XY: 0.293 AC XY: 21796 AN XY: 74414

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.275

Alfa AF: 0.202 Hom.: 7264

Bravo AF: 0.321

Asia WGS AF: 0.213 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.7
Dann	Benign	0.41

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

Other links and lift over

dbSNP: rs3799380; hg19: chr6-26467182;