rs6459193

Variant names:

• chr6-57341122-G-A
• rs6459193
• NM_000947.5:c.459+15077G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-57341122-G-A
• chr6-57341122-G-C

Variant summary

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

The NM_000947.5(PRIM2):​c.459+15077G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 151,952 control chromosomes in the GnomAD database, including 27,278 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 0.60 (27278 hom., cov: 31)
• Consequence: PRIM2 NM_000947.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336
• Publications: 6 publications found

Genes affected

PRIM2 (HGNC:9370): (DNA primase subunit 2) This gene encodes the 58 kilodalton subunit of DNA primase, an enzyme that plays a key role in the replication of DNA. The encoded protein forms a heterodimer with a 49 kilodalton subunit. This heterodimer functions as a DNA-directed RNA polymerase to synthesize small RNA primers that are used to create Okazaki fragments on the lagging strand of the DNA. Alternative splicing of this gene results in multiple transcript variants. This gene has a related pseudogene, which is also present on chromosome 6. [provided by RefSeq, Apr 2014]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000947.5. 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
	PRIM2	NM_000947.5	MANE Select	c.459+15077G>A		intron	N/A	NP_000938.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRIM2	ENST00000615550.5	TSL:1 MANE Select	c.459+15077G>A		intron	N/A	ENSP00000484105.1
	PRIM2	ENST00000672107.1		c.459+15077G>A		intron	N/A	ENSP00000500708.1
	PRIM2	ENST00000671770.1		c.459+15077G>A		intron	N/A	ENSP00000500602.1

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90826 AN: 151834 Hom.: 27247 Cov.: 31

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.598 AC: 90901 AN: 151952 Hom.: 27278 Cov.: 31 AF XY: 0.596 AC XY: 44291 AN XY: 74258

African (AFR) AF: 0.629 AC: 26066 AN: 41438

American (AMR) AF: 0.537 AC: 8192 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2111 AN: 3466

East Asian (EAS) AF: 0.491 AC: 2532 AN: 5162

South Asian (SAS) AF: 0.704 AC: 3390 AN: 4816

European-Finnish (FIN) AF: 0.602 AC: 6348 AN: 10538

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40335 AN: 67966

Other (OTH) AF: 0.582 AC: 1227 AN: 2108

Alfa AF: 0.590 Hom.: 39847

Bravo AF: 0.587

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.53
DANN	Benign	0.54
PhyloP100		-0.34
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: rs6459193; hg19: chr6-57205920;