NM_006995.5:c.95-150C>G

Variant names:

• chr6-26384865-C-G
• rs2072806
• NM_006995.5:c.95-150C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 24 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=-0.77).
• 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 rank	MANE	Protein	UniProt
BTN2A2	NM_006995.5	c.95-150C>G		intron_variant	Intron 2 of 7	ENST00000356709.9	NP_008926.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTN2A2	ENST00000356709.9	c.95-150C>G		intron_variant	Intron 2 of 7	1	NM_006995.5	ENSP00000349143.4

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

African (AFR) AF: 0.0343 AC: 577 AN: 16822

American (AMR) AF: 0.0362 AC: 687 AN: 18972

Ashkenazi Jewish (ASJ) AF: 0.0452 AC: 690 AN: 15260

East Asian (EAS) AF: 0.134 AC: 4325 AN: 32200

South Asian (SAS) AF: 0.0917 AC: 4470 AN: 48754

European-Finnish (FIN) AF: 0.0831 AC: 2869 AN: 34506

Middle Eastern (MID) AF: 0.0473 AC: 183 AN: 3870

European-Non Finnish (NFE) AF: 0.117 AC: 58182 AN: 496428

Other (OTH) AF: 0.0926 AC: 3174 AN: 34290

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

African (AFR) AF: 0.0339 AC: 1408 AN: 41552

American (AMR) AF: 0.0391 AC: 599 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0415 AC: 144 AN: 3470

East Asian (EAS) AF: 0.103 AC: 533 AN: 5188

South Asian (SAS) AF: 0.101 AC: 488 AN: 4826

European-Finnish (FIN) AF: 0.0789 AC: 837 AN: 10610

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7633 AN: 68014

Other (OTH) AF: 0.0664 AC: 140 AN: 2110

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
PhyloP100		0.16
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: rs2072806; hg19: chr6-26385093;