rs9357078

Positions:

• chr6-29329889-C-T

Variant summary

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

The ENST00000441966.1(DDX6P1):​n.1173G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0921 in 511,786 control chromosomes in the GnomAD database, including 2,524 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 0.086 (666 hom., cov: 32)
  • Exomes 𝑓: 0.095 (1858 hom.)
• Consequence: DDX6P1 ENST00000441966.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.58

Genes affected

DDX6P1 (HGNC:13948): (DEAD-box helicase 6 pseudogene 1)

LOC105375005 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375005	XR_926670.1	n.219+4123G>A		intron_variant, non_coding_transcript_variant
LOC105375005	XR_001744074.1	n.355+1437G>A		intron_variant, non_coding_transcript_variant
LOC105375005	XR_001744075.1	n.219+4123G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDX6P1	ENST00000441966.1	n.1173G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0855 AC: 13007 AN: 152076 Hom.: 664 Cov.: 32

Gnomad AFR AF: 0.0332

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0909

Gnomad SAS AF: 0.0684

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0888

GnomAD4 exome AF: 0.0949 AC: 34139 AN: 359592 Hom.: 1858 Cov.: 0 AF XY: 0.0913 AC XY: 18857 AN XY: 206462

Gnomad4 AFR exome AF: 0.0299

Gnomad4 AMR exome AF: 0.129

Gnomad4 ASJ exome AF: 0.128

Gnomad4 EAS exome AF: 0.0882

Gnomad4 SAS exome AF: 0.0612

Gnomad4 FIN exome AF: 0.123

Gnomad4 NFE exome AF: 0.0997

Gnomad4 OTH exome AF: 0.0955

GnomAD4 genome AF: 0.0855 AC: 13014 AN: 152194 Hom.: 666 Cov.: 32 AF XY: 0.0870 AC XY: 6470 AN XY: 74400

Gnomad4 AFR AF: 0.0331

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0913

Gnomad4 SAS AF: 0.0686

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.0879

Alfa AF: 0.0985 Hom.: 796

Bravo AF: 0.0851

Asia WGS AF: 0.0760 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	10
DANN	Benign	0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9357078; hg19: chr6-29297666;