Variant chr5-180948368-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The ENST00000231229.8(BTNL8):c.931G>A(p.Gly311Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00081 ( 0 hom., cov: 25)

Exomes 𝑓: 0.000085 ( 10 hom. )

Failed GnomAD Quality Control

Consequence

BTNL8
ENST00000231229.8 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.650

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 Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0045530796).

BP6

Variant 5-180948368-G-A is Benign according to our data. Variant chr5-180948368-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2656160.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTNL8	NM_001040462.3 linkuse as main transcript	c.801G>A	p.Ala267=	synonymous_variant	5/8	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.801G>A	p.Ala267=	synonymous_variant	5/8	1	NM_001040462.3	ENSP00000342197	P1	Q6UX41-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

110

AN:

135038

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000303

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00132

Gnomad ASJ

AF:

0.000908

Gnomad EAS

AF:

0.00396

Gnomad SAS

AF:

0.00155

Gnomad FIN

AF:

0.000113

Gnomad MID

AF:

0.00345

Gnomad NFE

AF:

0.000834

Gnomad OTH

AF:

0.00162

GnomAD3 exomes

AF:

0.0000430

AC:

AN:

232672

Hom.:

AF XY:

0.0000554

AC XY:

AN XY:

126304

show subpopulations

Gnomad AFR exome

AF:

0.000188

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000678

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000845

AC:

112

AN:

1324942

Hom.:

Cov.:

AF XY:

0.0000923

AC XY:

AN XY:

660766

show subpopulations

Gnomad4 AFR exome

AF:

0.0000304

Gnomad4 AMR exome

AF:

0.000222

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000255

Gnomad4 SAS exome

AF:

0.0000354

Gnomad4 FIN exome

AF:

0.0000212

Gnomad4 NFE exome

AF:

0.0000781

Gnomad4 OTH exome

AF:

0.000199

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000814

AC:

110

AN:

135150

Hom.:

Cov.:

AF XY:

0.000774

AC XY:

AN XY:

65894

show subpopulations

Gnomad4 AFR

AF:

0.000302

Gnomad4 AMR

AF:

0.00132

Gnomad4 ASJ

AF:

0.000908

Gnomad4 EAS

AF:

0.00398

Gnomad4 SAS

AF:

0.00155

Gnomad4 FIN

AF:

0.000113

Gnomad4 NFE

AF:

0.000835

Gnomad4 OTH

AF:

0.00160

Alfa

AF:

0.0128

Hom.:

ExAC

AF:

0.000204

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

BTNL8: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.40

BayesDel_noAF

Benign

-0.54

CADD

Benign

DANN

Benign

0.72

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.00020

LIST_S2

Benign

0.31

MetaRNN

Benign

0.0046

MetaSVM

Benign

-0.91

MutationTaster

Benign

1.0

N;N;N;N;N;N;N

PROVEAN

Benign

0.040

REVEL

Benign

0.0010

Sift

Benign

0.13

Sift4G

Benign

0.18

Vest4

0.10

MutPred

0.25

Gain of MoRF binding (P = 0.0211);

MVP

0.092

ClinPred

0.0075

GERP RS

-0.026

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over