12-123614233-C-T

Variant names:

• chr12-123614233-C-T
• rs2048802
• NM_020936.3:c.825-952C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020936.3(DDX55):​c.825-952C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,116 control chromosomes in the GnomAD database, including 2,936 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 0.18 (2936 hom., cov: 32)
• Consequence: DDX55 NM_020936.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434

Genes affected

DDX55 (HGNC:20085): (DEAD-box helicase 55) This gene encodes a member of protein family containing a characteristic Asp-Glu-Ala-Asp (DEAD) motif. These proteins are putative RNA helicases, and may be involved in a range of nuclear processes including translational initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Multiple alternatively spliced transcript variants have been found for this gene. Pseudogenes have been identified on chromosomes 1 and 12. [provided by RefSeq, Feb 2016]

LOC105370041 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DDX55	NM_020936.3	c.825-952C>T		intron_variant	Intron 8 of 13	ENST00000238146.9	NP_065987.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DDX55	ENST00000238146.9	c.825-952C>T		intron_variant	Intron 8 of 13	1	NM_020936.3	ENSP00000238146.3

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27883 AN: 151998 Hom.: 2933 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.183 AC: 27898 AN: 152116 Hom.: 2936 Cov.: 32 AF XY: 0.178 AC XY: 13268 AN XY: 74390

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.169

Alfa AF: 0.137 Hom.: 1258

Bravo AF: 0.188

Asia WGS AF: 0.164 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.6
DANN	Benign	0.64

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

Other links and lift over

dbSNP: rs2048802; hg19: chr12-124098780;