6-60425399-A-T

Position:

• chr6-60425399-A-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000637553.1(PRIM2BP):​n.335A>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.173 in 1,530,890 control chromosomes in the GnomAD database, including 24,569 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.18 (2756 hom., cov: 31)
  • Exomes 𝑓: 0.17 (21813 hom.)
• Consequence: PRIM2BP ENST00000637553.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.00

Genes affected

PRIM2BP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRIM2BP		n.60425399A>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRIM2BP	ENST00000637553.1	n.335A>T		non_coding_transcript_exon_variant	4/9	6
ENSG00000290597	ENST00000649835.1	n.311-4988A>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28031 AN: 151868 Hom.: 2749 Cov.: 31

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.202

GnomAD3 exomes AF: 0.0826 AC: 14197 AN: 171900 Hom.: 0 AF XY: 0.0825 AC XY: 7554 AN XY: 91558

Gnomad AFR exome AF: 0.0944

Gnomad AMR exome AF: 0.0814

Gnomad ASJ exome AF: 0.0649

Gnomad EAS exome AF: 0.160

Gnomad SAS exome AF: 0.108

Gnomad FIN exome AF: 0.0556

Gnomad NFE exome AF: 0.0709

Gnomad OTH exome AF: 0.0789

GnomAD4 exome AF: 0.172 AC: 237407 AN: 1378904 Hom.: 21813 Cov.: 27 AF XY: 0.174 AC XY: 118014 AN XY: 679782

Gnomad4 AFR exome AF: 0.203

Gnomad4 AMR exome AF: 0.181

Gnomad4 ASJ exome AF: 0.161

Gnomad4 EAS exome AF: 0.296

Gnomad4 SAS exome AF: 0.235

Gnomad4 FIN exome AF: 0.123

Gnomad4 NFE exome AF: 0.164

Gnomad4 OTH exome AF: 0.183

GnomAD4 genome AF: 0.185 AC: 28069 AN: 151986 Hom.: 2756 Cov.: 31 AF XY: 0.188 AC XY: 13967 AN XY: 74282

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.206

Alfa AF: 0.157 Hom.: 234

Bravo AF: 0.192

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Uncertain	-0.030
CADD	Benign	17
DANN	Benign	0.89

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3763183; hg19: chr6-57393144;