rs1056667

Variant names:

• chr6-26510336-T-C
• rs1056667
• NM_001732.3:c.*1162T>C

Variant summary

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

The NM_001732.3(BTN1A1):​c.*1162T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 152,224 control chromosomes in the GnomAD database, including 19,452 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 0.50 (19442 hom., cov: 34)
  • Exomes 𝑓: 0.60 (10 hom.)
• Consequence: BTN1A1 NM_001732.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609
• Publications: 42 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTN1A1	NM_001732.3	c.*1162T>C		3_prime_UTR_variant	Exon 8 of 8	ENST00000684113.1	NP_001723.2
LOC107986583	XR_001744057.3	n.5890+11173A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTN1A1	ENST00000684113.1	c.*1162T>C		3_prime_UTR_variant	Exon 8 of 8		NM_001732.3	ENSP00000507193.1

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76327 AN: 152056 Hom.: 19421 Cov.: 34

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.512

GnomAD4 exome AF: 0.600 AC: 30 AN: 50 Hom.: 10 Cov.: 0 AF XY: 0.688 AC XY: 22 AN XY: 32

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.400 AC: 4 AN: 10

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.647 AC: 22 AN: 34

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.502 AC: 76400 AN: 152174 Hom.: 19442 Cov.: 34 AF XY: 0.503 AC XY: 37385 AN XY: 74384

African (AFR) AF: 0.521 AC: 21619 AN: 41516

American (AMR) AF: 0.562 AC: 8603 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1987 AN: 3472

East Asian (EAS) AF: 0.743 AC: 3849 AN: 5182

South Asian (SAS) AF: 0.556 AC: 2681 AN: 4824

European-Finnish (FIN) AF: 0.396 AC: 4195 AN: 10596

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31879 AN: 67970

Other (OTH) AF: 0.516 AC: 1089 AN: 2110

Alfa AF: 0.491 Hom.: 50359

Bravo AF: 0.514

Asia WGS AF: 0.642 AC: 2229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.32
PhyloP100		-0.61
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1056667; hg19: chr6-26510564; COSMIC: COSV55066929; COSMIC: COSV55066929;