3-128470729-C-T

Variant names:

• chr3-128470729-C-T
• rs2953128
• ENST00000471626.1:n.349-139C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

DNAJB8-AS1 (HGNC:41029): (DNAJB8 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000471626.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJB8-AS1	NR_037890.1		n.349-139C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJB8-AS1	ENST00000471626.1	TSL:2	n.349-139C>T		intron	N/A
	DNAJB8-AS1	ENST00000746121.1		n.353-2246C>T		intron	N/A
	DNAJB8-AS1	ENST00000746122.1		n.199-2246C>T		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.372 AC: 29 AN: 78

Other (OTH) AF: 0.750 AC: 6 AN: 8

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

African (AFR) AF: 0.697 AC: 28923 AN: 41504

American (AMR) AF: 0.431 AC: 6597 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1437 AN: 3472

East Asian (EAS) AF: 0.562 AC: 2907 AN: 5176

South Asian (SAS) AF: 0.583 AC: 2813 AN: 4824

European-Finnish (FIN) AF: 0.357 AC: 3780 AN: 10600

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28214 AN: 67980

Other (OTH) AF: 0.489 AC: 1034 AN: 2116

Alfa AF: 0.435 Hom.: 29904

Bravo AF: 0.513

Asia WGS AF: 0.542 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.54
DANN	Benign	0.35
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2953128;

hg19: chr3-128189572;