dbSNP rs7711990: BTNL8:n.788A>G (chr5-180947898-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000514448.5(BTNL8):n.788A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 1,221,076 control chromosomes in the GnomAD database, including 106,864 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 0.47 ( 17546 hom., cov: 32)

Exomes 𝑓: 0.41 ( 89318 hom. )

Consequence

BTNL8
ENST00000514448.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.645

Publications

6 publications found

Variant links:

Genes affected

BTNL8 (HGNC:26131): (butyrophilin like 8) Predicted to enable signaling receptor binding activity. Predicted to be involved in T cell receptor signaling pathway and regulation of cytokine production. Predicted to be located in plasma membrane. Predicted to be active in external side of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

BTNL8 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 (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTNL8	NM_001040462.3 link	c.787+273A>G		intron_variant	Intron 4 of 7	ENST00000340184.9	NP_001035552.1	Q6UX41-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTNL8	ENST00000340184.9 link	c.787+273A>G		intron_variant	Intron 4 of 7	1	NM_001040462.3	ENSP00000342197.4		Q6UX41-1

Frequencies

GnomAD3 genomes

AF:

0.466

AC:

70842

AN:

152014

Hom.:

17508

Cov.:

show subpopulations

Gnomad AFR

AF:

0.632

Gnomad AMI

AF:

0.411

Gnomad AMR

AF:

0.438

Gnomad ASJ

AF:

0.232

Gnomad EAS

AF:

0.345

Gnomad SAS

AF:

0.263

Gnomad FIN

AF:

0.427

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.415

Gnomad OTH

AF:

0.434

GnomAD4 exome

AF:

0.406

AC:

433650

AN:

1068944

Hom.:

89318

Cov.:

AF XY:

0.399

AC XY:

212849

AN XY:

533010

show subpopulations

African (AFR)

AF:

0.645

AC:

15895

AN:

24650

American (AMR)

AF:

0.393

AC:

10940

AN:

27820

Ashkenazi Jewish (ASJ)

AF:

0.247

AC:

4453

AN:

18034

East Asian (EAS)

AF:

0.359

AC:

13402

AN:

37334

South Asian (SAS)

AF:

0.256

AC:

15673

AN:

61330

European-Finnish (FIN)

AF:

0.418

AC:

15058

AN:

36026

Middle Eastern (MID)

AF:

0.343

AC:

1419

AN:

4134

European-Non Finnish (NFE)

AF:

0.416

AC:

338110

AN:

812914

Other (OTH)

AF:

0.400

AC:

18700

AN:

46702

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

12328

24655

36983

49310

61638

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9744

19488

29232

38976

48720

<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:

0.466

AC:

70933

AN:

152132

Hom.:

17546

Cov.:

AF XY:

0.462

AC XY:

34386

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.633

AC:

26248

AN:

41498

American (AMR)

AF:

0.438

AC:

6698

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.232

AC:

805

AN:

3472

East Asian (EAS)

AF:

0.346

AC:

1789

AN:

5174

South Asian (SAS)

AF:

0.264

AC:

1270

AN:

4818

European-Finnish (FIN)

AF:

0.427

AC:

4513

AN:

10562

Middle Eastern (MID)

AF:

0.381

AC:

112

AN:

294

European-Non Finnish (NFE)

AF:

0.415

AC:

28213

AN:

67988

Other (OTH)

AF:

0.430

AC:

910

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1863

3726

5590

7453

9316

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

622

1244

1866

2488

3110

<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:

0.456

Hom.:

2019

Bravo

AF:

0.472

Asia WGS

AF:

0.360

AC:

1250

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

4.1

(source)

DANN

Benign

0.66

PhyloP100

0.65

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