rs9357078

Variant names:

• chr6-29329889-C-T
• rs9357078
• ENST00000441966.1:n.1173G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

Genes affected

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

ENSG00000295863 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441966.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDX6P1	ENST00000441966.1	TSL:6	n.1173G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000295863	ENST00000733278.1		n.245+4123G>A		intron	N/A
	ENSG00000295863	ENST00000733279.1		n.269+2797G>A		intron	N/A

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

African (AFR) AF: 0.0299 AC: 304 AN: 10170

American (AMR) AF: 0.129 AC: 4369 AN: 33762

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 1445 AN: 11254

East Asian (EAS) AF: 0.0882 AC: 1157 AN: 13114

South Asian (SAS) AF: 0.0612 AC: 4015 AN: 65588

European-Finnish (FIN) AF: 0.123 AC: 2466 AN: 20050

Middle Eastern (MID) AF: 0.0490 AC: 59 AN: 1204

European-Non Finnish (NFE) AF: 0.0997 AC: 18784 AN: 188330

Other (OTH) AF: 0.0955 AC: 1540 AN: 16120

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

African (AFR) AF: 0.0331 AC: 1374 AN: 41534

American (AMR) AF: 0.113 AC: 1730 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3468

East Asian (EAS) AF: 0.0913 AC: 473 AN: 5180

South Asian (SAS) AF: 0.0686 AC: 331 AN: 4824

European-Finnish (FIN) AF: 0.130 AC: 1379 AN: 10570

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7024 AN: 68004

Other (OTH) AF: 0.0879 AC: 186 AN: 2116

Alfa AF: 0.0940 Hom.: 1402

Bravo AF: 0.0851

Asia WGS AF: 0.0760 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	10
DANN	Benign	0.52
PhyloP100		5.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9357078;

hg19: chr6-29297666;