6-60425399-A-T

Variant names:

• chr6-60425399-A-T
• rs3763183
• ENST00000637553.1:n.335A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

Genes affected

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

ENSG00000290597 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PRIM2BP		n.60425399A>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRIM2BP	ENST00000637553.1	n.335A>T		non_coding_transcript_exon_variant	Exon 4 of 9	6
ENSG00000290597	ENST00000812929.1	n.218A>T		non_coding_transcript_exon_variant	Exon 3 of 8
ENSG00000290597	ENST00000812931.1	n.177A>T		non_coding_transcript_exon_variant	Exon 3 of 7

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

GnomAD2 exomes AF: 0.0826 AC: 14197 AN: 171900 AF XY: 0.0825

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 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

African (AFR) AF: 0.203 AC: 6272 AN: 30972

American (AMR) AF: 0.181 AC: 6227 AN: 34326

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 3989 AN: 24720

East Asian (EAS) AF: 0.296 AC: 10449 AN: 35278

South Asian (SAS) AF: 0.235 AC: 17496 AN: 74452

European-Finnish (FIN) AF: 0.123 AC: 5952 AN: 48354

Middle Eastern (MID) AF: 0.211 AC: 1177 AN: 5568

European-Non Finnish (NFE) AF: 0.164 AC: 175402 AN: 1068168

Other (OTH) AF: 0.183 AC: 10443 AN: 57066

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

African (AFR) AF: 0.199 AC: 8246 AN: 41462

American (AMR) AF: 0.212 AC: 3235 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 608 AN: 3470

East Asian (EAS) AF: 0.309 AC: 1597 AN: 5168

South Asian (SAS) AF: 0.251 AC: 1201 AN: 4782

European-Finnish (FIN) AF: 0.132 AC: 1392 AN: 10564

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11106 AN: 67964

Other (OTH) AF: 0.206 AC: 432 AN: 2102

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
PhyloP100		5.0
Varity_R		0.26
Mutation Taster		=46/54	disease causing

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

Other links and lift over

dbSNP: rs3763183; hg19: chr6-57393144;