XM_047418987.1:c.-10+35448T>G

Variant names:

• chr6-57257165-T-G
• rs13213618
• XM_047418987.1:c.-10+35448T>G

Variant summary

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

The XM_047418987.1(PRIM2):​c.-10+35448T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,104 control chromosomes in the GnomAD database, including 5,977 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 0.24 (5977 hom., cov: 33)
• Consequence: PRIM2 XM_047418987.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564
• Publications: 2 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35770 AN: 151986 Hom.: 5961 Cov.: 33

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0321

Gnomad SAS AF: 0.0915

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.236 AC: 35828 AN: 152104 Hom.: 5977 Cov.: 33 AF XY: 0.227 AC XY: 16914 AN XY: 74386

African (AFR) AF: 0.474 AC: 19642 AN: 41426

American (AMR) AF: 0.126 AC: 1933 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 446 AN: 3472

East Asian (EAS) AF: 0.0322 AC: 167 AN: 5184

South Asian (SAS) AF: 0.0920 AC: 444 AN: 4826

European-Finnish (FIN) AF: 0.118 AC: 1247 AN: 10588

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11372 AN: 68002

Other (OTH) AF: 0.194 AC: 410 AN: 2110

Alfa AF: 0.243 Hom.: 907

Bravo AF: 0.246

Asia WGS AF: 0.0820 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.65
DANN	Benign	0.41
PhyloP100		-0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs13213618; hg19: chr6-57121963;