chr3-112498887-G-A

Variant names:

• chr3-112498887-G-A
• rs1844089
• NM_181780.4:c.88+384C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181780.4(BTLA):​c.88+384C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,004 control chromosomes in the GnomAD database, including 8,073 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 0.24 (8073 hom., cov: 31)
• Consequence: BTLA NM_181780.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304
• Publications: 13 publications found

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]

ENSG00000303317 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181780.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTLA	NM_181780.4	MANE Select	c.88+384C>T		intron	N/A	NP_861445.4
	BTLA	NM_001085357.2		c.88+384C>T		intron	N/A	NP_001078826.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTLA	ENST00000334529.10	TSL:1 MANE Select	c.88+384C>T		intron	N/A	ENSP00000333919.5
	BTLA	ENST00000383680.5	TSL:1	c.88+384C>T		intron	N/A	ENSP00000373178.4
	ENSG00000303317	ENST00000793585.1		n.393-19121G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36912 AN: 151884 Hom.: 8035 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.0700

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.0819

Gnomad OTH AF: 0.221

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.243 AC: 37000 AN: 152004 Hom.: 8073 Cov.: 31 AF XY: 0.242 AC XY: 17961 AN XY: 74314

African (AFR) AF: 0.575 AC: 23825 AN: 41416

American (AMR) AF: 0.251 AC: 3837 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3468

East Asian (EAS) AF: 0.245 AC: 1265 AN: 5158

South Asian (SAS) AF: 0.178 AC: 858 AN: 4814

European-Finnish (FIN) AF: 0.0700 AC: 741 AN: 10584

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.0818 AC: 5564 AN: 67982

Other (OTH) AF: 0.218 AC: 460 AN: 2106

Alfa AF: 0.176 Hom.: 613

Bravo AF: 0.277

Asia WGS AF: 0.218 AC: 756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.44
DANN	Benign	0.69
PhyloP100		-0.30
PromoterAI		0.021	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1844089; hg19: chr3-112217734;