chr6-26472427-A-G

Position:

• chr6-26472427-A-G

Variant summary

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

The NM_001197234.3(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 NM_001197234.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390

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=-0.82).
• 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/exons	MANE	Protein	UniProt
BTN2A1	NM_001197234.3	c.983-3695A>G		intron_variant			NP_001184163.1
LOC285819	NR_038992.1	n.2655-234T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTN2A1	ENST00000469185.5	c.983-3695A>G		intron_variant		1		ENSP00000419043.1
BTN2A1	ENST00000480218.1	c.227-3734A>G		intron_variant		3		ENSP00000418936.1
ENSG00000291336	ENST00000707189.1	n.1000-80760A>G		intron_variant
ENSG00000291338	ENST00000707191.1	n.1001-60278A>G		intron_variant

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

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.524

Alfa AF: 0.589 Hom.: 39068

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7763910; hg19: chr6-26472655;