rs6929846

chr6-26458037-T-C

Variant summary

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

The NM_007049.5(BTN2A1):c.-136T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 152,156 control chromosomes in the GnomAD database, including 40,102 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 0.71 (40102 hom., cov: 33)
  • Exomes 𝑓: 0.79 (67 hom.)
  • Failed GnomAD Quality Control
• Consequence: BTN2A1 NM_007049.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

Genes affected

BTN2A1 (HGNC:1136): (butyrophilin subfamily 2 member A1) This gene encodes a member of the immunoglobulin superfamily. The gene is located in a cluster of butyrophilin-like genes in the juxta-telomeric region of the major histocompatibility complex on chromosome 6. A pseudogene of this gene has been identified in this cluster. The encoded protein is an integral plasma membrane protein involved in lipid, fatty-acid, and sterol metabolism. Alterations in this gene may be associated with several disease states including metabolic syndrome. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2013]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTN2A1	NM_007049.5	c.-136T>C		5_prime_UTR_variant	1/8	ENST00000312541.10
BTN2A1	NM_001197233.3	c.-207T>C		5_prime_UTR_variant	1/7
BTN2A1	NM_001197234.3	c.-136T>C		5_prime_UTR_variant	1/8
BTN2A1	NM_078476.4	c.-136T>C		5_prime_UTR_variant	1/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTN2A1	ENST00000312541.10	c.-136T>C		5_prime_UTR_variant	1/8	1	NM_007049.5	P1
	ENST00000707189.1	n.1000-95150T>C		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1001-74668T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107730 AN: 152038 Hom.: 40092 Cov.: 33

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.701

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.789 AC: 161 AN: 204 Hom.: 67 Cov.: 0 AF XY: 0.794 AC XY: 108 AN XY: 136

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.788

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.795

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.708 AC: 107768 AN: 152156 Hom.: 40102 Cov.: 33 AF XY: 0.711 AC XY: 52928 AN XY: 74406

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.913

Gnomad4 SAS AF: 0.777

Gnomad4 FIN AF: 0.834

Gnomad4 NFE AF: 0.812

Gnomad4 OTH AF: 0.704

Alfa AF: 0.781 Hom.: 47080

Bravo AF: 0.685

Asia WGS AF: 0.828 AC: 2879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	6.6
Dann	Benign	0.65
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs6929846; hg19: chr6-26458265;