rs4730250

chr7-107567250-A-G

Variant summary

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

The NM_181581.3(DUS4L):c.116+64A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 1,432,380 control chromosomes in the GnomAD database, including 19,894 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 0.12 (1477 hom., cov: 32)
  • Exomes 𝑓: 0.17 (18417 hom.)
• Consequence: DUS4L NM_181581.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291

Genes affected

DUS4L (HGNC:21517): (dihydrouridine synthase 4 like) Predicted to enable tRNA dihydrouridine synthase activity. Predicted to be involved in tRNA dihydrouridine synthesis. [provided by Alliance of Genome Resources, Apr 2022]

DUS4L-BCAP29 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DUS4L	NM_181581.3	c.116+64A>G		intron_variant		ENST00000265720.8
DUS4L-BCAP29	NR_163940.2	n.503+64A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DUS4L	ENST00000265720.8	c.116+64A>G		intron_variant		2	NM_181581.3	P1

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18921 AN: 152074 Hom.: 1479 Cov.: 32

Gnomad AFR AF: 0.0335

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.124

GnomAD4 exome AF: 0.168 AC: 214648 AN: 1280188 Hom.: 18417 AF XY: 0.167 AC XY: 107113 AN XY: 641860

Gnomad4 AFR exome AF: 0.0276

Gnomad4 AMR exome AF: 0.141

Gnomad4 ASJ exome AF: 0.166

Gnomad4 EAS exome AF: 0.116

Gnomad4 SAS exome AF: 0.140

Gnomad4 FIN exome AF: 0.157

Gnomad4 NFE exome AF: 0.179

Gnomad4 OTH exome AF: 0.151

GnomAD4 genome AF: 0.124 AC: 18915 AN: 152192 Hom.: 1477 Cov.: 32 AF XY: 0.123 AC XY: 9160 AN XY: 74390

Gnomad4 AFR AF: 0.0334

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.124

Alfa AF: 0.163 Hom.: 2531

Bravo AF: 0.121

Asia WGS AF: 0.147 AC: 512 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	9.3
Dann	Benign	0.64
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs4730250; hg19: chr7-107207695; COSMIC: COSV51751917; COSMIC: COSV51751917;