17-63785824-G-T

Variant names:

• chr17-63785824-G-T
• rs2044125
• NM_203499.3:c.-16-1210G>T

Variant summary

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

The NM_203499.3(DDX42):​c.-16-1210G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 152,020 control chromosomes in the GnomAD database, including 38,773 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 0.70 (38773 hom., cov: 31)
• Consequence: DDX42 NM_203499.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 16 publications found

Genes affected

DDX42 (HGNC:18676): (DEAD-box helicase 42) This gene encodes a member of the Asp-Glu-Ala-Asp (DEAD) box protein family. Members of this protein family are putative RNA helicases, and are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. Two transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq, Jul 2008]

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 (AFR) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DDX42	NM_203499.3	c.-16-1210G>T		intron_variant	Intron 1 of 17	ENST00000389924.7	NP_987095.1
DDX42	NM_007372.3	c.-16-1210G>T		intron_variant	Intron 2 of 18		NP_031398.2
DDX42	XM_047435281.1	c.-16-1210G>T		intron_variant	Intron 3 of 19		XP_047291237.1
DDX42	XM_047435282.1	c.-16-1210G>T		intron_variant	Intron 4 of 20		XP_047291238.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DDX42	ENST00000389924.7	c.-16-1210G>T		intron_variant	Intron 1 of 17	5	NM_203499.3	ENSP00000374574.2

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106417 AN: 151902 Hom.: 38713 Cov.: 31

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.635

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.701 AC: 106534 AN: 152020 Hom.: 38773 Cov.: 31 AF XY: 0.701 AC XY: 52086 AN XY: 74290

African (AFR) AF: 0.918 AC: 38113 AN: 41508

American (AMR) AF: 0.635 AC: 9694 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1893 AN: 3472

East Asian (EAS) AF: 0.580 AC: 2994 AN: 5166

South Asian (SAS) AF: 0.747 AC: 3597 AN: 4816

European-Finnish (FIN) AF: 0.644 AC: 6790 AN: 10548

Middle Eastern (MID) AF: 0.655 AC: 190 AN: 290

European-Non Finnish (NFE) AF: 0.610 AC: 41441 AN: 67946

Other (OTH) AF: 0.657 AC: 1384 AN: 2106

Alfa AF: 0.658 Hom.: 5700

Bravo AF: 0.706

Asia WGS AF: 0.686 AC: 2382 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.20
PhyloP100		0.22
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: rs2044125; hg19: chr17-61863184;