chr6-26458297-C-G

Variant names:

• chr6-26458297-C-G
• rs2273193
• NM_007049.5:c.-31+155C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007049.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTN2A1	NM_007049.5	MANE Select	c.-31+155C>G		intron	N/A	NP_008980.1
	BTN2A1	NM_001197233.3		c.-102+155C>G		intron	N/A	NP_001184162.1
	BTN2A1	NM_078476.4		c.-31+155C>G		intron	N/A	NP_510961.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTN2A1	ENST00000312541.10	TSL:1 MANE Select	c.-31+155C>G		intron	N/A	ENSP00000312158.5
	BTN2A1	ENST00000429381.5	TSL:1	c.-31+155C>G		intron	N/A	ENSP00000416945.1
	BTN2A1	ENST00000469185.5	TSL:1	c.-31+155C>G		intron	N/A	ENSP00000419043.1

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

African (AFR) AF: 0.659 AC: 27308 AN: 41448

American (AMR) AF: 0.756 AC: 11554 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2466 AN: 3472

East Asian (EAS) AF: 0.835 AC: 4297 AN: 5146

South Asian (SAS) AF: 0.677 AC: 3263 AN: 4820

European-Finnish (FIN) AF: 0.782 AC: 8253 AN: 10560

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51292 AN: 67964

Other (OTH) AF: 0.737 AC: 1553 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.48
PhyloP100		-0.53
PromoterAI		-0.20	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2273193; hg19: chr6-26458525;