rs897669

Variant names:

• chr5-55263144-G-A
• rs897669
• NM_019030.4:c.3526-212C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019030.4. 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
	DHX29	NM_019030.4	MANE Select	c.3526-212C>T		intron	N/A	NP_061903.2
	DHX29	NM_001345964.2		c.3373-212C>T		intron	N/A	NP_001332893.1
	DHX29	NM_001345965.2		c.1618-212C>T		intron	N/A	NP_001332894.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DHX29	ENST00000251636.10	TSL:1 MANE Select	c.3526-212C>T		intron	N/A	ENSP00000251636.5
	DHX29	ENST00000504778.5	TSL:1	n.3734-212C>T		intron	N/A
	CCNO-DT	ENST00000506435.2	TSL:3	n.129-16389G>A		intron	N/A

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

African (AFR) AF: 0.120 AC: 4958 AN: 41430

American (AMR) AF: 0.121 AC: 1854 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.00519 AC: 18 AN: 3470

East Asian (EAS) AF: 0.0668 AC: 345 AN: 5164

South Asian (SAS) AF: 0.0882 AC: 423 AN: 4794

European-Finnish (FIN) AF: 0.0241 AC: 253 AN: 10508

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.0172 AC: 1170 AN: 67940

Other (OTH) AF: 0.0542 AC: 114 AN: 2102

Alfa AF: 0.0306 Hom.: 92

Bravo AF: 0.0695

Asia WGS AF: 0.0970 AC: 339 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.44
PhyloP100		0.11
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs897669; hg19: chr5-54558972;