rs1056667

Positions:

• chr6-26510336-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.94).
• 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/exons	MANE	UniProt
BTN1A1	NM_001732.3	c.*1162T>C		3_prime_UTR_variant	8/8	ENST00000684113.1
LOC107986583	XR_001744057.3	n.5890+11173A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTN1A1	ENST00000684113.1	c.*1162T>C		3_prime_UTR_variant	8/8		NM_001732.3	P1
BTN1A1	ENST00000244513.10	c.*1162T>C		3_prime_UTR_variant	7/7	1		P1
	ENST00000707189.1	n.1000-42851T>C		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1001-22369T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 0.647

Gnomad4 OTH exome AF: 0.500

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

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.516

Alfa AF: 0.481 Hom.: 17006

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1056667; hg19: chr6-26510564; COSMIC: COSV55066929; COSMIC: COSV55066929;