rs9358938

Positions:

• chr6-26387318-C-T

Variant summary

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

The NM_006995.5(BTN2A2):​c.443-695C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0785 in 152,212 control chromosomes in the GnomAD database, including 588 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 (588 hom., cov: 31)
• Consequence: BTN2A2 NM_006995.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972

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=-0.9).
• 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	Protein	UniProt
BTN2A2	NM_006995.5	c.443-695C>T		intron_variant		ENST00000356709.9	NP_008926.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTN2A2	ENST00000356709.9	c.443-695C>T		intron_variant		1	NM_006995.5	ENSP00000349143.4

Frequencies

GnomAD3 genomes AF: 0.0786 AC: 11960 AN: 152096 Hom.: 590 Cov.: 31

Gnomad AFR AF: 0.0339

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.0391

Gnomad ASJ AF: 0.0415

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0789

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0659

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

GnomAD4 genome AF: 0.0785 AC: 11951 AN: 152212 Hom.: 588 Cov.: 31 AF XY: 0.0758 AC XY: 5639 AN XY: 74402

Gnomad4 AFR AF: 0.0339

Gnomad4 AMR AF: 0.0389

Gnomad4 ASJ AF: 0.0415

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.0789

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.0662

Alfa AF: 0.105 Hom.: 589

Bravo AF: 0.0731

Asia WGS AF: 0.103 AC: 358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.29
DANN	Benign	0.28

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: rs9358938; hg19: chr6-26387546;