3-128472098-C-A

Variant names:

• chr3-128472098-C-A
• rs7431368
• ENST00000471626.1:n.1579C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000471626.1(DNAJB8-AS1):​n.1579C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.819 in 152,212 control chromosomes in the GnomAD database, including 51,198 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 0.82 (51189 hom., cov: 32)
  • Exomes 𝑓: 0.83 (9 hom.)
• Consequence: DNAJB8-AS1 ENST00000471626.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590
• Publications: 2 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.816 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJB8-AS1	NR_037890.1		n.1579C>A		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJB8-AS1	ENST00000471626.1	TSL:2	n.1579C>A		non_coding_transcript_exon	Exon 3 of 3
	DNAJB8-AS1	ENST00000746121.1		n.353-877C>A		intron	N/A
	DNAJB8-AS1	ENST00000746122.1		n.199-877C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.819 AC: 124559 AN: 152070 Hom.: 51144 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.818

GnomAD4 exome AF: 0.833 AC: 20 AN: 24 Hom.: 9 Cov.: 0 AF XY: 0.938 AC XY: 15 AN XY: 16

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.900 AC: 9 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 3 AN: 6

Other (OTH) AF: 1.00 AC: 8 AN: 8

GnomAD4 genome AF: 0.819 AC: 124663 AN: 152188 Hom.: 51189 Cov.: 32 AF XY: 0.822 AC XY: 61195 AN XY: 74412

African (AFR) AF: 0.822 AC: 34126 AN: 41504

American (AMR) AF: 0.828 AC: 12669 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2855 AN: 3472

East Asian (EAS) AF: 0.795 AC: 4117 AN: 5176

South Asian (SAS) AF: 0.828 AC: 3997 AN: 4826

European-Finnish (FIN) AF: 0.898 AC: 9527 AN: 10604

Middle Eastern (MID) AF: 0.777 AC: 227 AN: 292

European-Non Finnish (NFE) AF: 0.805 AC: 54722 AN: 68002

Other (OTH) AF: 0.817 AC: 1723 AN: 2108

Alfa AF: 0.809 Hom.: 193346

Bravo AF: 0.816

Asia WGS AF: 0.808 AC: 2808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.43
DANN	Benign	0.68
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs7431368; hg19: chr3-128190941;