Variant rs7711990 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001040462.3(BTNL8):c.787+273A>G variant causes a intron 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
NM_001040462.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.645

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 made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
BTNL8	NM_001040462.3 linkuse as main transcript	c.787+273A>G		intron_variant		ENST00000340184.9	NP_001035552.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTNL8	ENST00000340184.9 linkuse as main transcript	c.787+273A>G		intron_variant		1	NM_001040462.3	ENSP00000342197	P1	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

Gnomad4 AFR exome

AF:

0.645

Gnomad4 AMR exome

AF:

0.393

Gnomad4 ASJ exome

AF:

0.247

Gnomad4 EAS exome

AF:

0.359

Gnomad4 SAS exome

AF:

0.256

Gnomad4 FIN exome

AF:

0.418

Gnomad4 NFE exome

AF:

0.416

Gnomad4 OTH exome

AF:

0.400

GnomAD4 genome

AF:

0.466

AC:

70933

AN:

152132

Hom.:

17546

Cov.:

AF XY:

0.462

AC XY:

34386

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.633

Gnomad4 AMR

AF:

0.438

Gnomad4 ASJ

AF:

0.232

Gnomad4 EAS

AF:

0.346

Gnomad4 SAS

AF:

0.264

Gnomad4 FIN

AF:

0.427

Gnomad4 NFE

AF:

0.415

Gnomad4 OTH

AF:

0.430

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

DANN

Benign

0.66

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over