rs9467745

Variant names:

• chr6-26386534-G-A
• rs9467745
• NM_006995.5:c.442+1172G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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]

ENSG00000291336 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006995.5. 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
	BTN2A2	NM_006995.5	MANE Select	c.442+1172G>A		intron	N/A	NP_008926.2
	BTN2A2	NM_001197237.2		c.442+1172G>A		intron	N/A	NP_001184166.1
	BTN2A2	NM_181531.3		c.95-1479G>A		intron	N/A	NP_853509.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTN2A2	ENST00000356709.9	TSL:1 MANE Select	c.442+1172G>A		intron	N/A	ENSP00000349143.4
	BTN2A2	ENST00000416795.6	TSL:1	c.442+1172G>A		intron	N/A	ENSP00000399308.2
	BTN2A2	ENST00000469230.5	TSL:1	c.442+1172G>A		intron	N/A	ENSP00000417472.1

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

African (AFR) AF: 0.598 AC: 24758 AN: 41430

American (AMR) AF: 0.249 AC: 3802 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 618 AN: 3468

East Asian (EAS) AF: 0.132 AC: 683 AN: 5178

South Asian (SAS) AF: 0.122 AC: 587 AN: 4830

European-Finnish (FIN) AF: 0.233 AC: 2457 AN: 10546

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11934 AN: 67980

Other (OTH) AF: 0.285 AC: 603 AN: 2114

Alfa AF: 0.219 Hom.: 5117

Bravo AF: 0.319

Asia WGS AF: 0.149 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.47
DANN	Benign	0.25
PhyloP100		-2.7
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: rs9467745; hg19: chr6-26386762;