rs17539219

Variant names:

• chr6-26440314-T-G
• rs17539219
• ENST00000707189.1:n.1000-112873T>G

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.1000-112873T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,196 control chromosomes in the GnomAD database, including 2,266 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 0.17 (2266 hom., cov: 32)
• Consequence: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47

Genes affected

ENSG00000291336 (HGNC:):

BTN3A3 (HGNC:1140): (butyrophilin subfamily 3 member A3) 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., BTN2A1; MIM 613590) and BTN3 (e.g., BNT3A3) 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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTN3A3	NM_006994.5	c.-401T>G		upstream_gene_variant		ENST00000244519.7	NP_008925.1
BTN3A3	NM_197974.3	c.-456T>G		upstream_gene_variant			NP_932078.2
BTN3A3	NM_001242803.2	c.-376T>G		upstream_gene_variant			NP_001229732.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTN3A3	ENST00000244519.7	c.-401T>G		upstream_gene_variant		1	NM_006994.5	ENSP00000244519.2

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25700 AN: 152080 Hom.: 2263 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.0323

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.169 AC: 25728 AN: 152196 Hom.: 2266 Cov.: 32 AF XY: 0.170 AC XY: 12630 AN XY: 74416

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.0328

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.156

Alfa AF: 0.170 Hom.: 2223

Bravo AF: 0.169

Asia WGS AF: 0.115 AC: 399 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	1.8
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17539219; hg19: chr6-26440542;