rs3829284

Positions:

• chr6-153939055-A-G
• chr6-153939055-A-T

Variant summary

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

The variant allele was found at a frequency of 0.211 in 262,440 control chromosomes in the GnomAD database, including 5,963 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 0.19 (2949 hom., cov: 33)
  • Exomes 𝑓: 0.24 (3014 hom.)
• Consequence: HMGB3P19 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

Genes affected

HMGB3P19 (HGNC:39311): (high mobility group box 3 pseudogene 19)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HMGB3P19		n.153939055A>G		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29250 AN: 152122 Hom.: 2952 Cov.: 33

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.193

GnomAD4 exome AF: 0.236 AC: 26007 AN: 110200 Hom.: 3014 AF XY: 0.238 AC XY: 15329 AN XY: 64436

Gnomad4 AFR exome AF: 0.175

Gnomad4 AMR exome AF: 0.276

Gnomad4 ASJ exome AF: 0.242

Gnomad4 EAS exome AF: 0.350

Gnomad4 SAS exome AF: 0.362

Gnomad4 FIN exome AF: 0.220

Gnomad4 NFE exome AF: 0.193

Gnomad4 OTH exome AF: 0.228

GnomAD4 genome AF: 0.192 AC: 29249 AN: 152240 Hom.: 2949 Cov.: 33 AF XY: 0.200 AC XY: 14920 AN XY: 74434

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.191

Alfa AF: 0.183 Hom.: 436

Bravo AF: 0.189

Asia WGS AF: 0.348 AC: 1212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.6
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3829284; hg19: chr6-154260190;