rs2076030

Positions:

• chr6-26426628-G-A
• chr6-26426628-G-C

Variant summary

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

The NR_027795.1(BTN2A3P):​n.1452+105G>A variant causes a intron, non coding transcript 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 NR_027795.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226

Genes affected

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]

(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 = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTN2A3P	NR_027795.1	n.1452+105G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTN2A3P	ENST00000377662.6	n.706+105G>A		intron_variant, non_coding_transcript_variant
BTN2A3P	ENST00000686357.1	n.1367+105G>A		intron_variant, non_coding_transcript_variant
	ENST00000707189.1	n.1000-126559G>A		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1001-106077G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR exome AF: 0.0354

Gnomad4 AMR exome AF: 0.0321

Gnomad4 ASJ exome AF: 0.0412

Gnomad4 EAS exome AF: 0.123

Gnomad4 SAS exome AF: 0.0921

Gnomad4 FIN exome AF: 0.0832

Gnomad4 NFE exome AF: 0.107

Gnomad4 OTH exome AF: 0.0870

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

Gnomad4 AFR AF: 0.0334

Gnomad4 AMR AF: 0.0377

Gnomad4 ASJ AF: 0.0375

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.0983

Gnomad4 FIN AF: 0.0771

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.0635

Alfa AF: 0.0952 Hom.: 740

Bravo AF: 0.0711

Asia WGS AF: 0.105 AC: 363 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	2.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2076030; hg19: chr6-26426856;