6-153939055-A-G

Variant names:

• chr6-153939055-A-G
• rs3829284

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000403971.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HMGB3P19	ENST00000403971.2	TSL:6	n.-63T>C		upstream_gene	N/A

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 v4.9

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;