Genetic Variant 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:

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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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514448.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BTNL8	NM_001040462.3	MANE Select	c.787+273A>G	intron	N/A	NP_001035552.1
BTNL8	NM_001159707.2		c.439+273A>G	intron	N/A	NP_001153179.1
BTNL8	NM_001159709.2		c.412+273A>G	intron	N/A	NP_001153181.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BTNL8	ENST00000514448.5	TSL:1	n.788A>G	non_coding_transcript_exon	Exon 3 of 3
BTNL8	ENST00000340184.9	TSL:1 MANE Select	c.787+273A>G	intron	N/A	ENSP00000342197.4
BTNL8	ENST00000511704.5	TSL:1	c.439+273A>G	intron	N/A	ENSP00000425207.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over