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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRIM2BP		n.60425399A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRIM2BP	ENST00000637553.1	n.335A>C		non_coding_transcript_exon_variant	Exon 4 of 9	6
ENSG00000290597	ENST00000812929.1	n.218A>C		non_coding_transcript_exon_variant	Exon 3 of 8
ENSG00000290597	ENST00000812931.1	n.177A>C		non_coding_transcript_exon_variant	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 v4.3

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;