chr6-60391410-T-G

Variant names:

• chr6-60391410-T-G
• rs1358815

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.328 in 151,876 control chromosomes in the GnomAD database, including 8,976 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 0.33 (8976 hom., cov: 31)
• Consequence: PRIM2BP intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.789

Genes affected

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

ENSG00000290597 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=6.481).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRIM2BP		n.60391410T>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRIM2BP	ENST00000637553.1	n.235-8841T>G		intron_variant	Intron 2 of 8	6
ENSG00000290597	ENST00000649835.1	n.243-8841T>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49852 AN: 151760 Hom.: 8973 Cov.: 31

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.328 AC: 49863 AN: 151876 Hom.: 8976 Cov.: 31 AF XY: 0.329 AC XY: 24387 AN XY: 74208

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.359

Alfa AF: 0.337 Hom.: 914

Bravo AF: 0.329

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	6.5

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1358815; hg19: -;