6-30660305-A-G

Variant summary

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

The NM_003587.5(DHX16):​c.1545-63T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.923 in 1,340,388 control chromosomes in the GnomAD database, including 571,334 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 0.94 ( 67708 hom., cov: 31)
Exomes 𝑓: 0.92 ( 503626 hom. )

Consequence

DHX16
NM_003587.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.286
Variant links:
Genes affected
DHX16 (HGNC:2739): (DEAH-box helicase 16) 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 is a functional homolog of fission yeast Prp8 protein involved in cell cycle progression. This gene is mapped to the MHC region on chromosome 6p21.3, a region where many malignant, genetic and autoimmune disease genes are linked. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2018]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DHX16NM_003587.5 linkuse as main transcriptc.1545-63T>C intron_variant ENST00000376442.8 NP_003578.2 O60231Q5SQH4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DHX16ENST00000376442.8 linkuse as main transcriptc.1545-63T>C intron_variant 1 NM_003587.5 ENSP00000365625.3 O60231
DHX16ENST00000376437.9 linkuse as main transcriptc.102-63T>C intron_variant 1 ENSP00000365620.5 Q5SQH5
DHX16ENST00000480966.1 linkuse as main transcriptn.273T>C non_coding_transcript_exon_variant 1/32

Frequencies

GnomAD3 genomes
AF:
0.942
AC:
143356
AN:
152144
Hom.:
67651
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.985
Gnomad AMI
AF:
0.957
Gnomad AMR
AF:
0.952
Gnomad ASJ
AF:
0.957
Gnomad EAS
AF:
0.996
Gnomad SAS
AF:
0.984
Gnomad FIN
AF:
0.916
Gnomad MID
AF:
0.959
Gnomad NFE
AF:
0.910
Gnomad OTH
AF:
0.948
GnomAD4 exome
AF:
0.920
AC:
1093415
AN:
1188126
Hom.:
503626
Cov.:
15
AF XY:
0.922
AC XY:
538842
AN XY:
584408
show subpopulations
Gnomad4 AFR exome
AF:
0.987
Gnomad4 AMR exome
AF:
0.964
Gnomad4 ASJ exome
AF:
0.958
Gnomad4 EAS exome
AF:
0.998
Gnomad4 SAS exome
AF:
0.982
Gnomad4 FIN exome
AF:
0.914
Gnomad4 NFE exome
AF:
0.909
Gnomad4 OTH exome
AF:
0.929
GnomAD4 genome
AF:
0.942
AC:
143472
AN:
152262
Hom.:
67708
Cov.:
31
AF XY:
0.943
AC XY:
70160
AN XY:
74428
show subpopulations
Gnomad4 AFR
AF:
0.986
Gnomad4 AMR
AF:
0.952
Gnomad4 ASJ
AF:
0.957
Gnomad4 EAS
AF:
0.996
Gnomad4 SAS
AF:
0.983
Gnomad4 FIN
AF:
0.916
Gnomad4 NFE
AF:
0.910
Gnomad4 OTH
AF:
0.949
Alfa
AF:
0.920
Hom.:
67017
Bravo
AF:
0.948
Asia WGS
AF:
0.984
AC:
3424
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
6.8
DANN
Benign
0.75

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: rs3130000; hg19: chr6-30628082; API