6-26426628-G-A

Variant names:

• chr6-26426628-G-A
• rs2076030
• ENST00000466808.2:n.1067+105G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000466808.2(BTN2A3P):​n.1067+105G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0912 in 711,296 control chromosomes in the GnomAD database, including 3,620 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 0.077 (558 hom., cov: 31)
  • Exomes 𝑓: 0.095 (3062 hom.)
• Consequence: BTN2A3P ENST00000466808.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226
• Publications: 17 publications found

Genes affected

BTN2A3P (HGNC:):

BTN2A3P (HGNC:13229): (butyrophilin subfamily 2 member A3, pseudogene) The butyrophilin (BTN) genes are a group of major histocompatibility complex (MHC)-associated genes that encode type I membrane proteins with 2 extracellular immunoglobulin (Ig) domains and an intracellular B30.2 (PRYSPRY) domain. Three subfamilies of human BTN genes are located in the MHC class I region: the single-copy BTN1A1 gene (MIM 601610) and the BTN2 (e.g., BTN2A3) and BTN3 (e.g., BNT3A1; MIM 613593) genes, which have undergone tandem duplication, resulting in 3 copies of each (summary by Smith et al., 2010 [PubMed 20208008]).[supplied by OMIM, Nov 2010]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.107 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000466808.2. 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
	BTN2A3P	NR_027795.1		n.1452+105G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTN2A3P	ENST00000466808.2	TSL:1	n.1067+105G>A		intron	N/A
	BTN2A3P	ENST00000377662.6	TSL:6	n.706+105G>A		intron	N/A
	BTN2A3P	ENST00000463944.2	TSL:4	n.1433+105G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0768 AC: 11674 AN: 152074 Hom.: 559 Cov.: 31

Gnomad AFR AF: 0.0335

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.0379

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.0993

Gnomad FIN AF: 0.0771

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0632

GnomAD4 exome AF: 0.0952 AC: 53236 AN: 559104 Hom.: 3062 AF XY: 0.0959 AC XY: 28507 AN XY: 297220

African (AFR) AF: 0.0354 AC: 525 AN: 14826

American (AMR) AF: 0.0321 AC: 1026 AN: 31948

Ashkenazi Jewish (ASJ) AF: 0.0412 AC: 548 AN: 13304

East Asian (EAS) AF: 0.123 AC: 3224 AN: 26198

South Asian (SAS) AF: 0.0921 AC: 5362 AN: 58222

European-Finnish (FIN) AF: 0.0832 AC: 3217 AN: 38652

Middle Eastern (MID) AF: 0.0416 AC: 143 AN: 3440

European-Non Finnish (NFE) AF: 0.107 AC: 36850 AN: 345610

Other (OTH) AF: 0.0870 AC: 2341 AN: 26904

GnomAD4 genome AF: 0.0767 AC: 11667 AN: 152192 Hom.: 558 Cov.: 31 AF XY: 0.0740 AC XY: 5509 AN XY: 74412

African (AFR) AF: 0.0334 AC: 1388 AN: 41518

American (AMR) AF: 0.0377 AC: 577 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0375 AC: 130 AN: 3468

East Asian (EAS) AF: 0.100 AC: 520 AN: 5182

South Asian (SAS) AF: 0.0983 AC: 475 AN: 4830

European-Finnish (FIN) AF: 0.0771 AC: 817 AN: 10600

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7439 AN: 67986

Other (OTH) AF: 0.0635 AC: 134 AN: 2110

Alfa AF: 0.0907 Hom.: 905

Bravo AF: 0.0711

Asia WGS AF: 0.105 AC: 363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.60
PhyloP100		0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2076030; hg19: chr6-26426856;