NM_001732.3:c.-81G>T

Variant names:

• chr6-26500335-G-T
• rs13194984
• NM_001732.3:c.-81G>T

Variant summary

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

The NM_001732.3(BTN1A1):​c.-81G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0774 in 152,130 control chromosomes in the GnomAD database, including 655 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 0.077 (655 hom., cov: 32)
• Consequence: BTN1A1 NM_001732.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.691
• Publications: 33 publications found

Genes affected

BTN1A1 (HGNC:1135): (butyrophilin subfamily 1 member A1) Butyrophilin is the major protein associated with fat droplets in the milk. It is a member of the immunoglobulin superfamily. It may have a cell surface receptor function. The human butyrophilin gene is localized in the major histocompatibility complex (MHC) class I region of 6p and may have arisen relatively recently in evolution by the shuffling of exons between 2 ancestral gene families [provided by RefSeq, Jul 2008]

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 (NFE) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001732.3. 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
	BTN1A1	NM_001732.3	MANE Select	c.-81G>T		5_prime_UTR	Exon 1 of 8	NP_001723.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTN1A1	ENST00000684113.1	MANE Select	c.-81G>T		5_prime_UTR	Exon 1 of 8	ENSP00000507193.1
	ENSG00000291336	ENST00000707189.1		n.1000-52852G>T		intron	N/A
	ENSG00000291338	ENST00000707191.1		n.1001-32370G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0775 AC: 11776 AN: 152012 Hom.: 655 Cov.: 32

Gnomad AFR AF: 0.0230

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0511

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.00482

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.0815

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.0589

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

GnomAD4 genome AF: 0.0774 AC: 11777 AN: 152130 Hom.: 655 Cov.: 32 AF XY: 0.0729 AC XY: 5418 AN XY: 74356

African (AFR) AF: 0.0229 AC: 951 AN: 41506

American (AMR) AF: 0.0509 AC: 778 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0375 AC: 130 AN: 3470

East Asian (EAS) AF: 0.00483 AC: 25 AN: 5176

South Asian (SAS) AF: 0.0383 AC: 185 AN: 4830

European-Finnish (FIN) AF: 0.0815 AC: 861 AN: 10566

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8696 AN: 67990

Other (OTH) AF: 0.0588 AC: 124 AN: 2110

Alfa AF: 0.104 Hom.: 3671

Bravo AF: 0.0731

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.7
DANN	Benign	0.52
PhyloP100		0.69
PromoterAI		0.052	Neutral

Splicing

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

Other links and lift over

dbSNP: rs13194984; hg19: chr6-26500563;