rs2041992

Positions:

• chr19-46021213-C-T

Variant summary

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

The NM_005091.3(PGLYRP1):​c.287+1522G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,066 control chromosomes in the GnomAD database, including 10,586 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 0.36 (10586 hom., cov: 32)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: PGLYRP1 NM_005091.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472

Genes affected

PGLYRP1 (HGNC:8904): (peptidoglycan recognition protein 1) Enables peptidoglycan binding activity and peptidoglycan immune receptor activity. Involved in antimicrobial humoral immune response mediated by antimicrobial peptide; killing of cells of other organism; and response to bacterium. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

CCDC61 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PGLYRP1	NM_005091.3	c.287+1522G>A		intron_variant		ENST00000008938.5	NP_005082.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PGLYRP1	ENST00000008938.5	c.287+1522G>A		intron_variant		1	NM_005091.3	ENSP00000008938.3
CCDC61	ENST00000601763.1	n.186C>T		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55139 AN: 151942 Hom.: 10533 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.327

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.363 AC: 55262 AN: 152060 Hom.: 10586 Cov.: 32 AF XY: 0.362 AC XY: 26920 AN XY: 74332

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.335

Alfa AF: 0.346 Hom.: 5200

Bravo AF: 0.380

Asia WGS AF: 0.518 AC: 1798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.77
DANN	Benign	0.78
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs2041992; hg19: chr19-46524471;