chr7-100363571-A-G

Variant names:

• chr7-100363571-A-G
• rs6955367
• NM_178238.4:c.656-3778A>G

Variant summary

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

The NM_178238.4(PILRB):​c.656-3778A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,152 control chromosomes in the GnomAD database, including 3,412 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 0.20 (3412 hom., cov: 32)
• Consequence: PILRB NM_178238.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.847
• Publications: 40 publications found

Genes affected

PILRB (HGNC:18297): (paired immunoglobin like type 2 receptor beta) The paired immunoglobin-like type 2 receptors consist of highly related activating and inhibitory receptors that are involved in the regulation of many aspects of the immune system. The paired immunoglobulin-like receptor genes are located in a tandem head-to-tail orientation on chromosome 7. This gene encodes the activating member of the receptor pair and contains a truncated cytoplasmic tail relative to its inhibitory counterpart (PILRA), that has a long cytoplasmic tail with immunoreceptor tyrosine-based inhibitory (ITIM) motifs. This gene is thought to have arisen from a duplication of the inhibitory PILRA gene and evolved to acquire its activating function. [provided by RefSeq, Jun 2013]

STAG3L5P-PVRIG2P-PILRB (HGNC:48898): (STAG3L5P-PVRIG2P-PILRB readthrough) This locus represents naturally occurring readthrough transcription among the neighboring LOC101735302 (stromal antigen 3 pseudogene), LOC101752334 (poliovirus receptor related immunoglobulin domain containing pseudogene) and PILRB (paired immunoglobin-like type 2 receptor beta) genes on chromosome 7. The readthrough transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is unlikely to produce a protein product. [provided by RefSeq, Jun 2013]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178238.4. 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
	PILRB	NM_178238.4	MANE Select	c.656-3778A>G		intron	N/A	NP_839956.1
	PILRB	NM_001371931.2		c.826+2188A>G		intron	N/A	NP_001358860.1
	STAG3L5P-PVRIG2P-PILRB	NR_036569.1		n.3201-3778A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PILRB	ENST00000609309.3	TSL:1 MANE Select	c.656-3778A>G		intron	N/A	ENSP00000477365.1
	PILRB	ENST00000448382.5	TSL:2	c.813-3778A>G		intron	N/A	ENSP00000415775.1
	PILRB	ENST00000452089.5	TSL:2	c.656-3778A>G		intron	N/A	ENSP00000391748.1

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30835 AN: 152034 Hom.: 3391 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0338

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.203 AC: 30890 AN: 152152 Hom.: 3412 Cov.: 32 AF XY: 0.201 AC XY: 14955 AN XY: 74408

African (AFR) AF: 0.275 AC: 11387 AN: 41478

American (AMR) AF: 0.134 AC: 2040 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 780 AN: 3468

East Asian (EAS) AF: 0.0337 AC: 175 AN: 5192

South Asian (SAS) AF: 0.120 AC: 577 AN: 4828

European-Finnish (FIN) AF: 0.220 AC: 2331 AN: 10598

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12835 AN: 68002

Other (OTH) AF: 0.203 AC: 428 AN: 2112

Alfa AF: 0.187 Hom.: 1561

Bravo AF: 0.201

Asia WGS AF: 0.0930 AC: 325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.65
PhyloP100		-0.85
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: rs6955367; hg19: chr7-99961194;