rs7431368

Positions:

• chr3-128472098-C-A
• chr3-128472098-C-G
• chr3-128472098-C-T

Variant summary

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

The NR_037890.1(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 NR_037890.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJB8-AS1	NR_037890.1	n.1579C>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJB8-AS1	ENST00000471626.1	n.1579C>A		non_coding_transcript_exon_variant	3/3	2

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

Gnomad4 FIN exome AF: 0.900

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 1.00

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

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.828

Gnomad4 ASJ AF: 0.822

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.898

Gnomad4 NFE AF: 0.805

Gnomad4 OTH AF: 0.817

Alfa AF: 0.809 Hom.: 81273

Bravo AF: 0.816

Asia WGS AF: 0.808 AC: 2808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7431368; hg19: chr3-128190941;