rs17756426

Positions:

• chr6-73395696-A-C

Variant summary

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

The NM_018665.3(DDX43):​c.250+541A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0832 in 152,016 control chromosomes in the GnomAD database, including 598 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 0.083 (598 hom., cov: 31)
• Consequence: DDX43 NM_018665.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

Genes affected

DDX43 (HGNC:18677): (DEAD-box helicase 43) The protein encoded by this gene is an ATP-dependent RNA helicase in the DEAD-box family and displays tumor-specific expression. [provided by RefSeq, Jul 2008]

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 (SAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DDX43	NM_018665.3	c.250+541A>C		intron_variant		ENST00000370336.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DDX43	ENST00000370336.5	c.250+541A>C		intron_variant		1	NM_018665.3	P1
DDX43	ENST00000464221.1	n.262+541A>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0833 AC: 12650 AN: 151898 Hom.: 599 Cov.: 31

Gnomad AFR AF: 0.0460

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.0911

Gnomad ASJ AF: 0.0968

Gnomad EAS AF: 0.00962

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0975

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0832 AC: 12653 AN: 152016 Hom.: 598 Cov.: 31 AF XY: 0.0851 AC XY: 6326 AN XY: 74320

Gnomad4 AFR AF: 0.0460

Gnomad4 AMR AF: 0.0910

Gnomad4 ASJ AF: 0.0968

Gnomad4 EAS AF: 0.00984

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.0975

Gnomad4 OTH AF: 0.0805

Alfa AF: 0.0904 Hom.: 215

Bravo AF: 0.0784

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.64

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: rs17756426; hg19: chr6-74105419;