6-60391410-T-G

Variant names:

• chr6-60391410-T-G
• rs1358815

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ENSG00000290597 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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.235-8841T>G		intron	N/A
	ENSG00000290597	ENST00000649835.1		n.243-8841T>G		intron	N/A
	ENSG00000290597	ENST00000812932.1		n.233-8841T>G		intron	N/A

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

African (AFR) AF: 0.183 AC: 7588 AN: 41430

American (AMR) AF: 0.413 AC: 6289 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1078 AN: 3470

East Asian (EAS) AF: 0.520 AC: 2672 AN: 5142

South Asian (SAS) AF: 0.339 AC: 1632 AN: 4812

European-Finnish (FIN) AF: 0.355 AC: 3744 AN: 10532

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.377 AC: 25584 AN: 67932

Other (OTH) AF: 0.359 AC: 756 AN: 2108

Alfa AF: 0.264 Hom.: 1172

Bravo AF: 0.329

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	6.5
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs1358815;