9-5556786-A-G

Position:

• chr9-5556786-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_025239.4(PDCD1LG2):​c.632-832A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,902 control chromosomes in the GnomAD database, including 14,636 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 0.42 (14636 hom., cov: 31)
• Consequence: PDCD1LG2 NM_025239.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.523

Genes affected

PDCD1LG2 (HGNC:18731): (programmed cell death 1 ligand 2) Involved in negative regulation of activated T cell proliferation; negative regulation of interferon-gamma production; and negative regulation of interleukin-10 production. Predicted to be located in plasma membrane. Predicted to be active in external side of plasma membrane. Biomarker of pulmonary tuberculosis. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000286162 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDCD1LG2	NM_025239.4	c.632-832A>G		intron_variant		ENST00000397747.5	NP_079515.2
PDCD1LG2	XM_005251600.4	c.632-832A>G		intron_variant			XP_005251657.1
LOC124902114	XR_007061406.1	n.162-32157T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDCD1LG2	ENST00000397747.5	c.632-832A>G		intron_variant		1	NM_025239.4	ENSP00000380855.3
ENSG00000286162	ENST00000661858.1	n.183-32157T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63197 AN: 151784 Hom.: 14620 Cov.: 31

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.416 AC: 63255 AN: 151902 Hom.: 14636 Cov.: 31 AF XY: 0.413 AC XY: 30695 AN XY: 74264

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.401

Alfa AF: 0.319 Hom.: 7309

Bravo AF: 0.433

Asia WGS AF: 0.391 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.81

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

Other links and lift over

dbSNP: rs1009759; hg19: chr9-5556786;