Genetic Variant BTN3A2:c.*2159G>A (chr6-26377921-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_007047.5(BTN3A2):c.*2159G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,460 control chromosomes in the GnomAD database, including 2,042 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 0.16 ( 2036 hom., cov: 32)

Exomes 𝑓: 0.11 ( 6 hom. )

Consequence

BTN3A2
NM_007047.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0160

Publications

13 publications found

Variant links:

Genes affected

BTN3A2 (HGNC:1139): (butyrophilin subfamily 3 member A2) This gene encodes a member of the immunoglobulin superfamily, which resides in the juxta-telomeric region of the major histocompatability class 1 locus and is clustered with the other family members on chromosome 6. The encoded protein may be involved in the adaptive immune response. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2013]

BTN3A2 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007047.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BTN3A2	NM_007047.5	MANE Select	c.*2159G>A	3_prime_UTR	Exon 11 of 11	NP_008978.2
BTN3A2	NM_001197246.2		c.*1427G>A	3_prime_UTR	Exon 9 of 9	NP_001184175.1
BTN3A2	NM_001197247.3		c.*2441G>A	3_prime_UTR	Exon 11 of 11	NP_001184176.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BTN3A2	ENST00000377708.7	TSL:1 MANE Select	c.*2159G>A	3_prime_UTR	Exon 11 of 11	ENSP00000366937.2
BTN3A2	ENST00000356386.6	TSL:5	c.*1427G>A	3_prime_UTR	Exon 11 of 11	ENSP00000348751.2
BTN3A2	ENST00000396934.7	TSL:2	c.*2159G>A	3_prime_UTR	Exon 9 of 9	ENSP00000380140.3

Frequencies

GnomAD3 genomes

AF:

0.159

AC:

24096

AN:

152012

Hom.:

2037

Cov.:

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.167

Gnomad AMR

AF:

0.151

Gnomad ASJ

AF:

0.179

Gnomad EAS

AF:

0.0434

Gnomad SAS

AF:

0.176

Gnomad FIN

AF:

0.135

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.135

Gnomad OTH

AF:

0.144

GnomAD4 exome

AF:

0.114

AC:

AN:

332

Hom.:

Cov.:

AF XY:

0.118

AC XY:

AN XY:

170

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.0938

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.125

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.115

AC:

AN:

270

Other (OTH)

AF:

0.125

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.590

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.159

AC:

24115

AN:

152128

Hom.:

2036

Cov.:

AF XY:

0.157

AC XY:

11690

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.218

AC:

9027

AN:

41466

American (AMR)

AF:

0.151

AC:

2309

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.179

AC:

623

AN:

3472

East Asian (EAS)

AF:

0.0439

AC:

227

AN:

5176

South Asian (SAS)

AF:

0.177

AC:

851

AN:

4818

European-Finnish (FIN)

AF:

0.135

AC:

1432

AN:

10582

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.135

AC:

9149

AN:

67998

Other (OTH)

AF:

0.142

AC:

300

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

999

1999

2998

3998

4997

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<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:

0.134

Hom.:

1303

Bravo

AF:

0.162

Asia WGS

AF:

0.0930

AC:

324

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.6

(source)

DANN

Benign

0.71

PhyloP100

-0.016

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over