Genetic Variant BTN1A1:c.*1162T>C (chr6-26510336-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.609

Publications

42 publications found

Variant links:

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]

BTN1A1 links:

ENSG00000291336 (HGNC:):

ENSG00000291336 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

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.*1162T>C		3_prime_UTR	Exon 8 of 8	NP_001723.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BTN1A1	ENST00000684113.1	MANE Select	c.*1162T>C	3_prime_UTR	Exon 8 of 8	ENSP00000507193.1
BTN1A1	ENST00000244513.10	TSL:1	c.*1162T>C	3_prime_UTR	Exon 7 of 7	ENSP00000244513.6
ENSG00000291336	ENST00000707189.1		n.1000-42851T>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.502

AC:

76327

AN:

152056

Hom.:

19421

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.688

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.400

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.647

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.502

AC:

76400

AN:

152174

Hom.:

19442

Cov.:

AF XY:

0.503

AC XY:

37385

AN XY:

74384

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

2017

4034

6050

8067

10084

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

684

1368

2052

2736

3420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.3

(source)

DANN

Benign

0.32

PhyloP100

-0.61

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over