rs897669

chr5-55263144-G-A

Variant summary

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

The NM_019030.4(DHX29):c.3526-212C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0605 in 151,876 control chromosomes in the GnomAD database, including 487 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 0.060 (487 hom., cov: 31)
• Consequence: DHX29 NM_019030.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110

Genes affected

DHX29 (HGNC:15815): (DExH-box helicase 29) This gene encodes a member of the DEAH (Asp-Glu-Ala-His) subfamily of proteins, part of the DEAD (Asp-Glu-Ala-Asp) box family of RNA helicases. The encoded protein functions in translation initiation, and is specifically required for ribosomal scanning across stable mRNA secondary structures during initiation codon selection. This protein may also play a role in sensing virally derived cytosolic nucleic acids. Knockdown of this gene results in reduced protein translation and impaired proliferation of cancer cells. [provided by RefSeq, Sep 2016]

CCNO-DT (HGNC:55543): (CCNO divergent transcript)

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 (AMR) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DHX29	NM_019030.4	c.3526-212C>T		intron_variant		ENST00000251636.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DHX29	ENST00000251636.10	c.3526-212C>T		intron_variant		1	NM_019030.4	P1
DHX29	ENST00000504778.5	n.3734-212C>T		intron_variant, non_coding_transcript_variant		1
CCNO-DT	ENST00000506435.1	n.108-16389G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0603 AC: 9156 AN: 151774 Hom.: 485 Cov.: 31

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.00519

Gnomad EAS AF: 0.0666

Gnomad SAS AF: 0.0886

Gnomad FIN AF: 0.0241

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0172

Gnomad OTH AF: 0.0548

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0605 AC: 9184 AN: 151876 Hom.: 487 Cov.: 31 AF XY: 0.0623 AC XY: 4622 AN XY: 74208

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.00519

Gnomad4 EAS AF: 0.0668

Gnomad4 SAS AF: 0.0882

Gnomad4 FIN AF: 0.0241

Gnomad4 NFE AF: 0.0172

Gnomad4 OTH AF: 0.0542

Alfa AF: 0.0302 Hom.: 75

Bravo AF: 0.0695

Asia WGS AF: 0.0970 AC: 339 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.8
Dann	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs897669; hg19: chr5-54558972;