rs2041992

Variant names:

• chr19-46021213-C-T
• rs2041992
• NM_005091.3:c.287+1522G>A

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:33629): (coiled-coil domain containing 61) Enables identical protein binding activity and microtubule binding activity. Involved in centriole assembly and mitotic spindle assembly. Located in centriolar satellite and ciliary basal body. Part of centriolar subdistal appendage. [provided by Alliance of Genome Resources, Apr 2022]

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 rank	MANE	Protein	UniProt
PGLYRP1	NM_005091.3	c.287+1522G>A		intron_variant	Intron 1 of 2	ENST00000008938.5	NP_005082.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PGLYRP1	ENST00000008938.5	c.287+1522G>A		intron_variant	Intron 1 of 2	1	NM_005091.3	ENSP00000008938.3
CCDC61	ENST00000601763.1	n.186C>T		non_coding_transcript_exon_variant	Exon 2 of 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;