chr12-123614233-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020936.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDX55	NM_020936.3	MANE Select	c.825-952C>T		intron	N/A	NP_065987.1
	DDX55	NR_135104.2		n.875-952C>T		intron	N/A
	DDX55	NR_135105.2		n.875-952C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDX55	ENST00000238146.9	TSL:1 MANE Select	c.825-952C>T		intron	N/A	ENSP00000238146.3
	DDX55	ENST00000538744.5	TSL:5	c.825-952C>T		intron	N/A	ENSP00000443114.1
	DDX55	ENST00000354291.8	TSL:5	n.*185-952C>T		intron	N/A	ENSP00000346244.4

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

African (AFR) AF: 0.287 AC: 11895 AN: 41476

American (AMR) AF: 0.121 AC: 1841 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3472

East Asian (EAS) AF: 0.114 AC: 588 AN: 5176

South Asian (SAS) AF: 0.164 AC: 788 AN: 4818

European-Finnish (FIN) AF: 0.112 AC: 1180 AN: 10576

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.156 AC: 10600 AN: 68010

Other (OTH) AF: 0.169 AC: 358 AN: 2116

Alfa AF: 0.148 Hom.: 2021

Bravo AF: 0.188

Asia WGS AF: 0.164 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.6
DANN	Benign	0.64
PhyloP100		0.43
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2048802; hg19: chr12-124098780;