chr6-57247330-G-A

Position:

• chr6-57247330-G-A

Variant summary

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

The XM_047418987.1(PRIM2):​c.-10+25613G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 152,006 control chromosomes in the GnomAD database, including 18,245 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 0.48 (18245 hom., cov: 32)
• Consequence: PRIM2 XM_047418987.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428

Genes affected

PRIM2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRIM2	XM_047418987.1	c.-10+25613G>A		intron_variant			XP_047274943.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73468 AN: 151888 Hom.: 18235 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.484 AC: 73512 AN: 152006 Hom.: 18245 Cov.: 32 AF XY: 0.486 AC XY: 36100 AN XY: 74288

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.497

Alfa AF: 0.461 Hom.: 33061

Bravo AF: 0.506

Asia WGS AF: 0.625 AC: 2175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	4.3
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7760349; hg19: chr6-57112128;