19-18920635-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_019070.5(DDX49):​c.171C>T​(p.Val57Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00222 in 1,611,850 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0015 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0023 ( 7 hom. )

Consequence

DDX49
NM_019070.5 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0300
Variant links:
Genes affected
DDX49 (HGNC:18684): (DEAD-box helicase 49) Enables RNA binding activity. Involved in positive regulation of cell growth and regulation of rRNA stability. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
Variant 19-18920635-C-T is Benign according to our data. Variant chr19-18920635-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2649602.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.03 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 7 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DDX49NM_019070.5 linkc.171C>T p.Val57Val synonymous_variant Exon 2 of 13 ENST00000247003.9 NP_061943.2 Q9Y6V7-1
DDX49XM_011528084.4 linkc.-211-16C>T intron_variant Intron 1 of 13 XP_011526386.1
DDX49NR_033677.2 linkn.143-16C>T intron_variant Intron 1 of 12

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DDX49ENST00000247003.9 linkc.171C>T p.Val57Val synonymous_variant Exon 2 of 13 1 NM_019070.5 ENSP00000247003.3 Q9Y6V7-1
ENSG00000268193ENST00000596918.5 linkn.*168-7589G>A intron_variant Intron 4 of 6 5 ENSP00000469669.1 M0R1B8

Frequencies

GnomAD3 genomes
AF:
0.00152
AC:
232
AN:
152180
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000434
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000851
Gnomad ASJ
AF:
0.00202
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00124
Gnomad FIN
AF:
0.00132
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00251
Gnomad OTH
AF:
0.00144
GnomAD3 exomes
AF:
0.00203
AC:
509
AN:
251340
Hom.:
1
AF XY:
0.00201
AC XY:
273
AN XY:
135852
show subpopulations
Gnomad AFR exome
AF:
0.000431
Gnomad AMR exome
AF:
0.000435
Gnomad ASJ exome
AF:
0.00308
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00128
Gnomad FIN exome
AF:
0.00208
Gnomad NFE exome
AF:
0.00315
Gnomad OTH exome
AF:
0.00228
GnomAD4 exome
AF:
0.00229
AC:
3343
AN:
1459552
Hom.:
7
Cov.:
30
AF XY:
0.00228
AC XY:
1653
AN XY:
725528
show subpopulations
Gnomad4 AFR exome
AF:
0.000359
Gnomad4 AMR exome
AF:
0.000448
Gnomad4 ASJ exome
AF:
0.00352
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00157
Gnomad4 FIN exome
AF:
0.00279
Gnomad4 NFE exome
AF:
0.00252
Gnomad4 OTH exome
AF:
0.00227
GnomAD4 genome
AF:
0.00152
AC:
232
AN:
152298
Hom.:
1
Cov.:
32
AF XY:
0.00133
AC XY:
99
AN XY:
74464
show subpopulations
Gnomad4 AFR
AF:
0.000433
Gnomad4 AMR
AF:
0.000850
Gnomad4 ASJ
AF:
0.00202
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00124
Gnomad4 FIN
AF:
0.00132
Gnomad4 NFE
AF:
0.00251
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.00261
Hom.:
2
Bravo
AF:
0.00142
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.00240
EpiControl
AF:
0.00190

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
May 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

DDX49: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.40
CADD
Benign
11
DANN
Benign
0.80

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.14
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs34332105; hg19: chr19-19031444; COSMIC: COSV99447387; COSMIC: COSV99447387; API