rs3763183

Variant names:

• chr6-60425399-A-C
• rs3763183
• ENST00000637553.1:n.335A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-60425399-A-C
• chr6-60425399-A-G
• chr6-60425399-A-T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The ENST00000637553.1(PRIM2BP):​n.335A>C variant causes a non coding transcript exon change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PRIM2BP ENST00000637553.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.00
• Publications: 13 publications found

Genes affected

PRIM2BP (HGNC:55759): (primase 2B, pseudogene)

ENSG00000290597 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637553.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRIM2BP	ENST00000637553.1	TSL:6	n.335A>C		non_coding_transcript_exon	Exon 4 of 9
	ENSG00000290597	ENST00000812929.1		n.218A>C		non_coding_transcript_exon	Exon 3 of 8
	ENSG00000290597	ENST00000812931.1		n.177A>C		non_coding_transcript_exon	Exon 3 of 7

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1383016 Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0 AN XY: 681902

African (AFR) AF: 0.00 AC: 0 AN: 31100

American (AMR) AF: 0.00 AC: 0 AN: 34542

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24792

East Asian (EAS) AF: 0.00 AC: 0 AN: 35388

South Asian (SAS) AF: 0.00 AC: 0 AN: 74804

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 48442

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5588

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1071098

Other (OTH) AF: 0.00 AC: 0 AN: 57262

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Uncertain	-0.050
CADD	Benign	17
DANN	Benign	0.91
PhyloP100		5.0
Varity_R		0.46
Mutation Taster		=42/58	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs3763183; hg19: chr6-57393144;