rs3829284

Variant names:

• chr6-153939055-A-G
• rs3829284

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
HMGB3P19		n.153939055A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HMGB3P19	ENST00000403971.2	n.-63T>C		upstream_gene_variant		6

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

African (AFR) AF: 0.175 AC: 557 AN: 3176

American (AMR) AF: 0.276 AC: 3074 AN: 11132

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 535 AN: 2214

East Asian (EAS) AF: 0.350 AC: 2280 AN: 6512

South Asian (SAS) AF: 0.362 AC: 5181 AN: 14328

European-Finnish (FIN) AF: 0.220 AC: 1225 AN: 5576

Middle Eastern (MID) AF: 0.207 AC: 62 AN: 300

European-Non Finnish (NFE) AF: 0.193 AC: 11900 AN: 61740

Other (OTH) AF: 0.228 AC: 1193 AN: 5222

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

African (AFR) AF: 0.164 AC: 6823 AN: 41546

American (AMR) AF: 0.252 AC: 3849 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 786 AN: 3470

East Asian (EAS) AF: 0.314 AC: 1623 AN: 5168

South Asian (SAS) AF: 0.356 AC: 1714 AN: 4820

European-Finnish (FIN) AF: 0.210 AC: 2233 AN: 10620

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11570 AN: 68008

Other (OTH) AF: 0.191 AC: 403 AN: 2108

Alfa AF: 0.182 Hom.: 443

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
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs3829284; hg19: chr6-154260190;