rs2072806

Positions:

• chr6-26384865-C-G

Variant summary

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

The NM_006995.5(BTN2A2):​c.95-150C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 853,386 control chromosomes in the GnomAD database, including 5,252 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 0.079 (592 hom., cov: 32)
  • Exomes 𝑓: 0.11 (4660 hom.)
• Consequence: BTN2A2 NM_006995.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157

Genes affected

BTN2A2 (HGNC:1137): (butyrophilin subfamily 2 member A2) Butyrophilin is the major protein associated with fat droplets in the milk. This gene is a member of the BTN2 subfamily of genes, which encode proteins belonging to the butyrophilin protein family. The gene is located in a cluster on chromosome 6, consisting of seven genes belonging to the expanding B7/butyrophilin-like group, a subset of the immunoglobulin gene superfamily. The encoded protein is a type I receptor glycoprotein involved in lipid, fatty-acid and sterol metabolism. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2010]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTN2A2	NM_006995.5	c.95-150C>G		intron_variant		ENST00000356709.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTN2A2	ENST00000356709.9	c.95-150C>G		intron_variant		1	NM_006995.5	P1
	ENST00000707189.1	n.1000-168322C>G		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1001-147840C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0788 AC: 11984 AN: 152166 Hom.: 594 Cov.: 32

Gnomad AFR AF: 0.0339

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.0393

Gnomad ASJ AF: 0.0415

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0789

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0661

GnomAD4 exome AF: 0.107 AC: 75157 AN: 701102 Hom.: 4660 AF XY: 0.106 AC XY: 37900 AN XY: 356050

Gnomad4 AFR exome AF: 0.0343

Gnomad4 AMR exome AF: 0.0362

Gnomad4 ASJ exome AF: 0.0452

Gnomad4 EAS exome AF: 0.134

Gnomad4 SAS exome AF: 0.0917

Gnomad4 FIN exome AF: 0.0831

Gnomad4 NFE exome AF: 0.117

Gnomad4 OTH exome AF: 0.0926

GnomAD4 genome AF: 0.0786 AC: 11975 AN: 152284 Hom.: 592 Cov.: 32 AF XY: 0.0759 AC XY: 5652 AN XY: 74460

Gnomad4 AFR AF: 0.0339

Gnomad4 AMR AF: 0.0391

Gnomad4 ASJ AF: 0.0415

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0789

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.0664

Alfa AF: 0.0988 Hom.: 99

Bravo AF: 0.0732

Asia WGS AF: 0.103 AC: 359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.0
DANN	Benign	0.73

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: rs2072806; hg19: chr6-26385093;