Genetic Variant NM_007242.7:c.1084C>G (chr16-70331782-C-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_007242.7(DDX19B):c.1084C>G(p.Leu362Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

DDX19B
NM_007242.7 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.807

Publications

0 publications found

Variant links:

Genes affected

DDX19B (HGNC:2742): (DEAD-box helicase 19B) DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They 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. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein, which exhibits RNA-dependent ATPase and ATP-dependent RNA-unwinding activities. This protein is recruited to the cytoplasmic fibrils of the nuclear pore complex, where it participates in the export of mRNA from the nucleus. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

DDX19B links:

ENSG00000260537 (HGNC:):

ENSG00000260537 links:

DDX19A-DT (HGNC:55349): (DDX19A divergent transcript)

DDX19A-DT links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.18540844).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007242.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
DDX19B	NM_007242.7	MANE Select	c.1084C>G	p.Leu362Val	missense	Exon 10 of 12	NP_009173.1	Q9UMR2-1
DDX19B	NM_001363938.1		c.1099C>G	p.Leu367Val	missense	Exon 10 of 12	NP_001350867.1	H3BQK0
DDX19B	NM_001257172.2		c.1006C>G	p.Leu336Val	missense	Exon 9 of 11	NP_001244101.1	Q9UMR2-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
DDX19B	ENST00000288071.11	TSL:1 MANE Select	c.1084C>G	p.Leu362Val	missense	Exon 10 of 12	ENSP00000288071.7	Q9UMR2-1
DDX19B	ENST00000355992.7	TSL:1	c.991C>G	p.Leu331Val	missense	Exon 9 of 11	ENSP00000348271.3	Q9UMR2-2
DDX19B	ENST00000393657.6	TSL:1	c.757C>G	p.Leu253Val	missense	Exon 8 of 10	ENSP00000377267.2	Q9UMR2-3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.25

BayesDel_addAF

Benign

-0.090

BayesDel_noAF

Benign

-0.37

CADD

Benign

(source)

DANN

Benign

0.93

DEOGEN2

Benign

0.17

Eigen

Benign

-0.70

Eigen_PC

Benign

-0.51

FATHMM_MKL

Benign

0.52

LIST_S2

Uncertain

0.94

M_CAP

Benign

0.022

MetaRNN

Benign

0.19

MetaSVM

Benign

-0.93

MutationAssessor

Benign

-0.30

PhyloP100

0.81

PrimateAI

Uncertain

0.73

PROVEAN

Benign

-0.92

REVEL

Benign

0.16

Sift

Benign

0.85

Sift4G

Benign

1.0

Polyphen

0.012

Vest4

0.43

MutPred

0.43

Gain of sheet (P = 0.0827)

MVP

0.47

MPC

0.72

ClinPred

0.62

GERP RS

3.9

Varity_R

0.26

gMVP

0.36

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over