rs11186426

Variant names:

• chr10-91053249-G-C
• rs11186426
• ENST00000450119.1:n.199G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

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

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

ENSG00000273124 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450119.1. 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
	LINC00502	NR_047467.2		n.359+5220G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDX18P6	ENST00000450119.1	TSL:6	n.199G>C		non_coding_transcript_exon	Exon 1 of 1
	LINC00502	ENST00000423621.2	TSL:3	n.814+5220G>C		intron	N/A
	ENSG00000273124	ENST00000607979.2	TSL:6	n.151-55421C>G		intron	N/A

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

African (AFR) AF: 0.405 AC: 1261 AN: 3116

American (AMR) AF: 0.0298 AC: 319 AN: 10702

Ashkenazi Jewish (ASJ) AF: 0.0293 AC: 95 AN: 3244

East Asian (EAS) AF: 0.00890 AC: 67 AN: 7530

South Asian (SAS) AF: 0.0465 AC: 563 AN: 12096

European-Finnish (FIN) AF: 0.0725 AC: 753 AN: 10380

Middle Eastern (MID) AF: 0.0527 AC: 33 AN: 626

European-Non Finnish (NFE) AF: 0.0696 AC: 5553 AN: 79764

Other (OTH) AF: 0.0826 AC: 576 AN: 6972

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

African (AFR) AF: 0.394 AC: 16330 AN: 41410

American (AMR) AF: 0.0703 AC: 1075 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0341 AC: 118 AN: 3462

East Asian (EAS) AF: 0.0110 AC: 57 AN: 5182

South Asian (SAS) AF: 0.0488 AC: 235 AN: 4816

European-Finnish (FIN) AF: 0.0740 AC: 783 AN: 10580

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0780 AC: 5306 AN: 67990

Other (OTH) AF: 0.119 AC: 252 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.60
DANN	Benign	0.46
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs11186426; hg19: chr10-92813006;