rs13194984

Positions:

• chr6-26500335-G-T

Variant summary

Our verdict is Benign. Variant got -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

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]

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTN1A1	NM_001732.3	c.-81G>T		5_prime_UTR_variant	1/8	ENST00000684113.1	NP_001723.2
LOC107986583	XR_001744057.3	n.5891-12191C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTN1A1	ENST00000684113.1	c.-81G>T		5_prime_UTR_variant	1/8		NM_001732.3	ENSP00000507193	P1
	ENST00000707189.1	n.1000-52852G>T		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1001-32370G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0229

Gnomad4 AMR AF: 0.0509

Gnomad4 ASJ AF: 0.0375

Gnomad4 EAS AF: 0.00483

Gnomad4 SAS AF: 0.0383

Gnomad4 FIN AF: 0.0815

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.0588

Alfa AF: 0.109 Hom.: 2336

Bravo AF: 0.0731

Asia WGS AF: 0.0230 AC: 81 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	8.7
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13194984; hg19: chr6-26500563;