6-26472427-A-G

Variant names:

• chr6-26472427-A-G
• rs7763910
• ENST00000469185.5:c.983-3695A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000469185.5(BTN2A1):​c.983-3695A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 152,072 control chromosomes in the GnomAD database, including 21,237 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 0.49 (21237 hom., cov: 32)
• Consequence: BTN2A1 ENST00000469185.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390
• Publications: 30 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTN2A1	NM_001197234.3	c.983-3695A>G		intron_variant	Intron 7 of 7		NP_001184163.1
LOC285819	NR_038992.1	n.2655-234T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTN2A1	ENST00000469185.5	c.983-3695A>G		intron_variant	Intron 7 of 7	1		ENSP00000419043.1
BTN2A1	ENST00000480218.1	c.227-3734A>G		intron_variant	Intron 3 of 3	3		ENSP00000418936.1
ENSG00000291336	ENST00000707189.1	n.1000-80760A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74572 AN: 151952 Hom.: 21223 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.491 AC: 74595 AN: 152072 Hom.: 21237 Cov.: 32 AF XY: 0.497 AC XY: 36932 AN XY: 74338

African (AFR) AF: 0.179 AC: 7450 AN: 41510

American (AMR) AF: 0.625 AC: 9541 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2446 AN: 3470

East Asian (EAS) AF: 0.707 AC: 3650 AN: 5166

South Asian (SAS) AF: 0.697 AC: 3361 AN: 4820

European-Finnish (FIN) AF: 0.550 AC: 5797 AN: 10546

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40568 AN: 67972

Other (OTH) AF: 0.524 AC: 1107 AN: 2114

Alfa AF: 0.558 Hom.: 56626

Bravo AF: 0.478

Asia WGS AF: 0.682 AC: 2370 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	9.3
DANN	Benign	0.73
PhyloP100		0.39
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7763910; hg19: chr6-26472655;