Genetic Variant ENST00000707189.1:n.1000-112763C>T (chr6-26440424-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000707189.1(ENSG00000291336):n.1000-112763C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,182 control chromosomes in the GnomAD database, including 1,199 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 0.12 ( 1199 hom., cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ENSG00000291336
ENST00000707189.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.43

Publications

7 publications found

Variant links:

Genes affected

ENSG00000291336 (HGNC:):

ENSG00000291336 links:

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:

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=-0.81).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
BTN3A3	NM_006994.5 link	c.-291C>T	upstream_gene_variant	ENST00000244519.7	NP_008925.1	O00478-1A0A024R042
BTN3A3	NM_197974.3 link	c.-346C>T	upstream_gene_variant		NP_932078.2	O00478-2
BTN3A3	NM_001242803.2 link	c.-266C>T	upstream_gene_variant		NP_001229732.1	O00478

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTN3A3	ENST00000244519.7 link	c.-291C>T		upstream_gene_variant		1	NM_006994.5	ENSP00000244519.2		O00478-1

Frequencies

GnomAD3 genomes

AF:

0.122

AC:

18627

AN:

152064

Hom.:

1194

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.189

Gnomad AMR

AF:

0.139

Gnomad ASJ

AF:

0.139

Gnomad EAS

AF:

0.0300

Gnomad SAS

AF:

0.156

Gnomad FIN

AF:

0.126

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.111

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

GnomAD4 genome

AF:

0.123

AC:

18654

AN:

152182

Hom.:

1199

Cov.:

AF XY:

0.123

AC XY:

9148

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.124

AC:

5129

AN:

41504

American (AMR)

AF:

0.140

AC:

2134

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.139

AC:

484

AN:

3470

East Asian (EAS)

AF:

0.0304

AC:

158

AN:

5192

South Asian (SAS)

AF:

0.158

AC:

762

AN:

4824

European-Finnish (FIN)

AF:

0.126

AC:

1337

AN:

10588

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.121

AC:

8210

AN:

68002

Other (OTH)

AF:

0.110

AC:

233

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

853

1705

2558

3410

4263

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

206

412

618

824

1030

<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:

0.121

Hom.:

1713

Bravo

AF:

0.123

Asia WGS

AF:

0.0780

AC:

271

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.6

(source)

DANN

Benign

0.67

PhyloP100

-1.4

PromoterAI

-0.16

Neutral

(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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over