rs17612333

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001012967.3(DDX60L):​c.2980-2527G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,124 control chromosomes in the GnomAD database, including 1,250 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 0.11 ( 1250 hom., cov: 32)

Consequence

DDX60L
NM_001012967.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.29
Variant links:
Genes affected
DDX60L (HGNC:26429): (DExD/H-box 60 like) This gene encodes a member of the DExD/H-box helicase family of proteins, a subset of the super family 2 helicases. Members of the DExD/H-box helicase family share a conserved functional core comprised of two RecA-like globular domains. These domains contain conserved motifs that mediate ATP binding, ATP hydrolysis, nucleic acid binding, and RNA unwinding. In addition to functions in RNA metabolism, members of this family are involved in anti-viral immunity and act as cytosolic sensors of viral nucleic acids. The protein encoded by this gene has been shown to inhibit hepatitis C virus replication in response to interferon stimulation in cell culture. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DDX60LNM_001012967.3 linkuse as main transcriptc.2980-2527G>T intron_variant ENST00000682922.1 NP_001012985.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DDX60LENST00000682922.1 linkuse as main transcriptc.2980-2527G>T intron_variant NM_001012967.3 ENSP00000507872
DDX60LENST00000505863.1 linkuse as main transcriptc.2068-2527G>T intron_variant 2 ENSP00000421026
DDX60LENST00000505890.5 linkuse as main transcriptc.2980-2527G>T intron_variant 2 ENSP00000422202
DDX60LENST00000511577.5 linkuse as main transcriptc.2980-2527G>T intron_variant 5 ENSP00000422423 P1

Frequencies

GnomAD3 genomes
AF:
0.109
AC:
16643
AN:
152006
Hom.:
1250
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0224
Gnomad AMI
AF:
0.0901
Gnomad AMR
AF:
0.150
Gnomad ASJ
AF:
0.0919
Gnomad EAS
AF:
0.138
Gnomad SAS
AF:
0.131
Gnomad FIN
AF:
0.232
Gnomad MID
AF:
0.0475
Gnomad NFE
AF:
0.132
Gnomad OTH
AF:
0.103
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.109
AC:
16637
AN:
152124
Hom.:
1250
Cov.:
32
AF XY:
0.115
AC XY:
8578
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.0223
Gnomad4 AMR
AF:
0.150
Gnomad4 ASJ
AF:
0.0919
Gnomad4 EAS
AF:
0.138
Gnomad4 SAS
AF:
0.132
Gnomad4 FIN
AF:
0.232
Gnomad4 NFE
AF:
0.132
Gnomad4 OTH
AF:
0.102
Alfa
AF:
0.0906
Hom.:
165
Bravo
AF:
0.101
Asia WGS
AF:
0.127
AC:
439
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.4
DANN
Benign
0.71

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

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

Other links and lift over

dbSNP: rs17612333; hg19: chr4-169330384; API