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 ENST00000812929.1(ENSG00000290597):​n.218A>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: ENSG00000290597 ENST00000812929.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812929.1. 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.335A>T		non_coding_transcript_exon	Exon 4 of 9
	ENSG00000290597	ENST00000812929.1		n.218A>T		non_coding_transcript_exon	Exon 3 of 8
	ENSG00000290597	ENST00000812931.1		n.177A>T		non_coding_transcript_exon	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 v4.9

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;