rs2953128

Positions:

• chr3-128470729-C-T

Variant summary

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

The ENST00000471626.1(DNAJB8-AS1):​n.349-139C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 152,262 control chromosomes in the GnomAD database, including 20,444 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 0.50 (20433 hom., cov: 33)
  • Exomes 𝑓: 0.44 (11 hom.)
• Consequence: DNAJB8-AS1 ENST00000471626.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

DNAJB8-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJB8-AS1	NR_037890.1	n.349-139C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJB8-AS1	ENST00000471626.1	n.349-139C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.500 AC: 76040 AN: 152048 Hom.: 20404 Cov.: 33

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.486

GnomAD4 exome AF: 0.436 AC: 41 AN: 94 Hom.: 11 AF XY: 0.456 AC XY: 31 AN XY: 68

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.372

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.500 AC: 76130 AN: 152168 Hom.: 20433 Cov.: 33 AF XY: 0.497 AC XY: 36993 AN XY: 74394

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.489

Alfa AF: 0.430 Hom.: 21238

Bravo AF: 0.513

Asia WGS AF: 0.542 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.54
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2953128; hg19: chr3-128189572;