dbSNP rs3846845: BTN3A3:c.433+383G>A (chr6-26444687-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_006994.5(BTN3A3):c.433+383G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 350,222 control chromosomes in the GnomAD database, including 41,794 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 0.53 ( 23450 hom., cov: 32)

Exomes 𝑓: 0.42 ( 18344 hom. )

Consequence

BTN3A3
NM_006994.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.389

Publications

7 publications found

Variant links:

Genes affected

BTN3A3 (HGNC:1140): (butyrophilin subfamily 3 member A3) The butyrophilin (BTN) genes are a group of major histocompatibility complex (MHC)-associated genes that encode type I membrane proteins with 2 extracellular immunoglobulin (Ig) domains and an intracellular B30.2 (PRYSPRY) domain. Three subfamilies of human BTN genes are located in the MHC class I region: the single-copy BTN1A1 gene (MIM 601610) and the BTN2 (e.g., BTN2A1; MIM 613590) and BTN3 (e.g., BNT3A3) genes, which have undergone tandem duplication, resulting in 3 copies of each (summary by Smith et al., 2010 [PubMed 20208008]).[supplied by OMIM, Nov 2010]

BTN3A3 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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
BTN3A3	NM_006994.5 link	c.433+383G>A	intron_variant	Intron 4 of 10	ENST00000244519.7	NP_008925.1	O00478-1A0A024R042
BTN3A3	NM_197974.3 link	c.307+383G>A	intron_variant	Intron 4 of 9		NP_932078.2	O00478-2
BTN3A3	NM_001242803.2 link	c.307+383G>A	intron_variant	Intron 2 of 5		NP_001229732.1	O00478

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTN3A3	ENST00000244519.7 link	c.433+383G>A		intron_variant	Intron 4 of 10	1	NM_006994.5	ENSP00000244519.2		O00478-1

Frequencies

GnomAD3 genomes

AF:

0.525

AC:

79792

AN:

152014

Hom.:

23405

Cov.:

show subpopulations

Gnomad AFR

AF:

0.804

Gnomad AMI

AF:

0.557

Gnomad AMR

AF:

0.442

Gnomad ASJ

AF:

0.370

Gnomad EAS

AF:

0.267

Gnomad SAS

AF:

0.406

Gnomad FIN

AF:

0.471

Gnomad MID

AF:

0.414

Gnomad NFE

AF:

0.419

Gnomad OTH

AF:

0.486

GnomAD4 exome

AF:

0.418

AC:

82876

AN:

198088

Hom.:

18344

Cov.:

AF XY:

0.415

AC XY:

43499

AN XY:

104800

show subpopulations

African (AFR)

AF:

0.818

AC:

5415

AN:

6618

American (AMR)

AF:

0.423

AC:

3165

AN:

7480

Ashkenazi Jewish (ASJ)

AF:

0.392

AC:

2274

AN:

5798

East Asian (EAS)

AF:

0.271

AC:

2730

AN:

10072

South Asian (SAS)

AF:

0.405

AC:

11331

AN:

28000

European-Finnish (FIN)

AF:

0.444

AC:

4058

AN:

9132

Middle Eastern (MID)

AF:

0.383

AC:

308

AN:

804

European-Non Finnish (NFE)

AF:

0.410

AC:

48960

AN:

119356

Other (OTH)

AF:

0.428

AC:

4635

AN:

10828

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

2267

4534

6802

9069

11336

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

372

744

1116

1488

1860

<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:

0.525

AC:

79888

AN:

152134

Hom.:

23450

Cov.:

AF XY:

0.521

AC XY:

38725

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.804

AC:

33409

AN:

41528

American (AMR)

AF:

0.441

AC:

6747

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.370

AC:

1283

AN:

3468

East Asian (EAS)

AF:

0.267

AC:

1381

AN:

5174

South Asian (SAS)

AF:

0.406

AC:

1955

AN:

4816

European-Finnish (FIN)

AF:

0.471

AC:

4973

AN:

10562

Middle Eastern (MID)

AF:

0.408

AC:

120

AN:

294

European-Non Finnish (NFE)

AF:

0.419

AC:

28497

AN:

67980

Other (OTH)

AF:

0.481

AC:

1015

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1719

3439

5158

6878

8597

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

660

1320

1980

2640

3300

<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:

0.475

Hom.:

5044

Bravo

AF:

0.539

Asia WGS

AF:

0.335

AC:

1166

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.69

(source)

DANN

Benign

0.56

PhyloP100

-0.39

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over