rs1796524

chr6-26448991-G-Achr6-26448991-G-T

Variant summary

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

The NM_006994.5(BTN3A3):c.964+237G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0856 in 151,946 control chromosomes in the GnomAD database, including 634 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 0.086 (634 hom., cov: 31)
• Consequence: BTN3A3 NM_006994.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

Genes affected

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTN3A3	NM_006994.5	c.964+237G>A		intron_variant		ENST00000244519.7
BTN3A3	NM_001242803.2	c.334+237G>A		intron_variant
BTN3A3	NM_197974.3	c.817+237G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTN3A3	ENST00000244519.7	c.964+237G>A		intron_variant		1	NM_006994.5	P1
	ENST00000707189.1	n.1000-104196G>A		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1001-83714G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0857 AC: 13006 AN: 151828 Hom.: 634 Cov.: 31

Gnomad AFR AF: 0.0536

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0880

Gnomad ASJ AF: 0.0796

Gnomad EAS AF: 0.0627

Gnomad SAS AF: 0.0565

Gnomad FIN AF: 0.0949

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0856 AC: 13012 AN: 151946 Hom.: 634 Cov.: 31 AF XY: 0.0857 AC XY: 6366 AN XY: 74270

Gnomad4 AFR AF: 0.0535

Gnomad4 AMR AF: 0.0879

Gnomad4 ASJ AF: 0.0796

Gnomad4 EAS AF: 0.0627

Gnomad4 SAS AF: 0.0569

Gnomad4 FIN AF: 0.0949

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0996

Alfa AF: 0.0923 Hom.: 272

Bravo AF: 0.0830

Asia WGS AF: 0.0640 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.62
Dann	Benign	0.36

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: rs1796524; hg19: chr6-26449219;