rs11186426

chr10-91053249-G-C

Variant summary

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

The ENST00000450119.1(DDX18P6):n.199G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 286,476 control chromosomes in the GnomAD database, including 4,153 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 0.16 (3556 hom., cov: 32)
  • Exomes 𝑓: 0.069 (597 hom.)
• Consequence: DDX18P6 ENST00000450119.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

Genes affected

DDX18P6 (HGNC:31126): (DEAD-box helicase 18 pseudogene 6)

LINC00502 (HGNC:43442): (long intergenic non-protein coding RNA 502)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00502	NR_047467.2	n.359+5220G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DDX18P6	ENST00000450119.1	n.199G>C		non_coding_transcript_exon_variant	1/1
LINC00502	ENST00000423621.2	n.814+5220G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24151 AN: 151928 Hom.: 3531 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0705

Gnomad ASJ AF: 0.0341

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.0496

Gnomad FIN AF: 0.0740

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0781

Gnomad OTH AF: 0.122

GnomAD4 exome AF: 0.0686 AC: 9220 AN: 134430 Hom.: 597 Cov.: 0 AF XY: 0.0679 AC XY: 5099 AN XY: 75056

Gnomad4 AFR exome AF: 0.405

Gnomad4 AMR exome AF: 0.0298

Gnomad4 ASJ exome AF: 0.0293

Gnomad4 EAS exome AF: 0.00890

Gnomad4 SAS exome AF: 0.0465

Gnomad4 FIN exome AF: 0.0725

Gnomad4 NFE exome AF: 0.0696

Gnomad4 OTH exome AF: 0.0826

GnomAD4 genome AF: 0.159 AC: 24216 AN: 152046 Hom.: 3556 Cov.: 32 AF XY: 0.154 AC XY: 11459 AN XY: 74356

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.0703

Gnomad4 ASJ AF: 0.0341

Gnomad4 EAS AF: 0.0110

Gnomad4 SAS AF: 0.0488

Gnomad4 FIN AF: 0.0740

Gnomad4 NFE AF: 0.0780

Gnomad4 OTH AF: 0.119

Alfa AF: 0.123 Hom.: 255

Bravo AF: 0.169

Asia WGS AF: 0.0540 AC: 189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.60
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11186426; hg19: chr10-92813006;