rs9467745

Positions:

• chr6-26386534-G-A

Variant summary

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

The NM_006995.5(BTN2A2):​c.442+1172G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,028 control chromosomes in the GnomAD database, including 9,531 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 (9531 hom., cov: 32)
• Consequence: BTN2A2 NM_006995.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66

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]

BTN2A2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTN2A2	NM_006995.5	c.442+1172G>A		intron_variant		ENST00000356709.9	NP_008926.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTN2A2	ENST00000356709.9	c.442+1172G>A		intron_variant		1	NM_006995.5	ENSP00000349143.4

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45566 AN: 151910 Hom.: 9496 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.300 AC: 45644 AN: 152028 Hom.: 9531 Cov.: 32 AF XY: 0.298 AC XY: 22154 AN XY: 74320

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.285

Alfa AF: 0.200 Hom.: 2975

Bravo AF: 0.319

Asia WGS AF: 0.149 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.47
DANN	Benign	0.25

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: rs9467745; hg19: chr6-26386762;