dbSNP rs1982809: BTLA:c.*2215T>C (chr3-112463893-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_181780.4(BTLA):c.*2215T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 333,754 control chromosomes in the GnomAD database, including 16,836 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 0.29 ( 7474 hom., cov: 32)

Exomes 𝑓: 0.29 ( 9362 hom. )

Consequence

BTLA
NM_181780.4 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.449

Variant links:

Genes affected

BTLA (HGNC:21087): (B and T lymphocyte associated) This gene encodes a member of the immunoglobulin superfamily. The encoded protein contains a single immunoglobulin (Ig) domain and is a receptor that relays inhibitory signals to suppress the immune response. Alternative splicing results in multiple transcript variants. Polymorphisms in this gene have been associated with an increased risk of rheumatoid arthritis. [provided by RefSeq, Aug 2011]

BTLA 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTLA	NM_181780.4 link	c.*2215T>C		downstream_gene_variant		ENST00000334529.10	NP_861445.4	Q7Z6A9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTLA	ENST00000334529.10 link	c.*2215T>C		downstream_gene_variant		1	NM_181780.4	ENSP00000333919.5		Q7Z6A9-1

Frequencies

GnomAD3 genomes

AF:

0.292

AC:

44432

AN:

151928

Hom.:

7453

Cov.:

show subpopulations

Gnomad AFR

AF:

0.291

Gnomad AMI

AF:

0.218

Gnomad AMR

AF:

0.408

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.753

Gnomad SAS

AF:

0.387

Gnomad FIN

AF:

0.298

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.227

Gnomad OTH

AF:

0.294

GnomAD4 exome

AF:

0.287

AC:

52087

AN:

181710

Hom.:

9362

AF XY:

0.284

AC XY:

26177

AN XY:

92118

show subpopulations

Gnomad4 AFR exome

AF:

0.273

Gnomad4 AMR exome

AF:

0.419

Gnomad4 ASJ exome

AF:

0.243

Gnomad4 EAS exome

AF:

0.728

Gnomad4 SAS exome

AF:

0.362

Gnomad4 FIN exome

AF:

0.263

Gnomad4 NFE exome

AF:

0.219

Gnomad4 OTH exome

AF:

0.285

GnomAD4 genome

AF:

0.293

AC:

44481

AN:

152044

Hom.:

7474

Cov.:

AF XY:

0.301

AC XY:

22363

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.291

Gnomad4 AMR

AF:

0.409

Gnomad4 ASJ

AF:

0.250

Gnomad4 EAS

AF:

0.753

Gnomad4 SAS

AF:

0.388

Gnomad4 FIN

AF:

0.298

Gnomad4 NFE

AF:

0.227

Gnomad4 OTH

AF:

0.300

Alfa

AF:

0.244

Hom.:

10006

Bravo

AF:

0.304

Asia WGS

AF:

0.540

AC:

1874

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.72

DANN

Benign

0.29

Splicing

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