6-26458297-C-G

Position:

• chr6-26458297-C-G

Variant summary

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

The NM_007049.5(BTN2A1):​c.-31+155C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.73 in 152,000 control chromosomes in the GnomAD database, including 40,695 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 0.73 (40695 hom., cov: 31)
• Consequence: BTN2A1 NM_007049.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530

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]

ENSG00000291336 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTN2A1	NM_007049.5	c.-31+155C>G		intron_variant		ENST00000312541.10	NP_008980.1
BTN2A1	NM_001197233.3	c.-102+155C>G		intron_variant			NP_001184162.1
BTN2A1	NM_078476.4	c.-31+155C>G		intron_variant			NP_510961.1
BTN2A1	NM_001197234.3	c.-31+155C>G		intron_variant			NP_001184163.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTN2A1	ENST00000312541.10	c.-31+155C>G		intron_variant		1	NM_007049.5	ENSP00000312158.5

Frequencies

GnomAD3 genomes AF: 0.730 AC: 110819 AN: 151882 Hom.: 40663 Cov.: 31

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.730 AC: 110902 AN: 152000 Hom.: 40695 Cov.: 31 AF XY: 0.732 AC XY: 54402 AN XY: 74292

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.755

Gnomad4 OTH AF: 0.737

Alfa AF: 0.742 Hom.: 5239

Bravo AF: 0.725

Asia WGS AF: 0.766 AC: 2666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.48

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: rs2273193; hg19: chr6-26458525;