rs7074242

Positions:

• chr10-91054988-G-A
• chr10-91054988-G-T

Variant summary

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

The ENST00000450119.1(DDX18P6):​n.1938G>A 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 0.346 in 463,956 control chromosomes in the GnomAD database, including 29,450 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 0.35 (9749 hom., cov: 33)
  • Exomes 𝑓: 0.34 (19701 hom.)
• Consequence: DDX18P6 ENST00000450119.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.627

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=-0.63).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00502	NR_047467.2	n.359+6959G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DDX18P6	ENST00000450119.1	n.1938G>A		non_coding_transcript_exon_variant	1/1
LINC00502	ENST00000423621.2	n.814+6959G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53743 AN: 151900 Hom.: 9737 Cov.: 33

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.340

GnomAD4 exome AF: 0.342 AC: 106781 AN: 311936 Hom.: 19701 Cov.: 0 AF XY: 0.353 AC XY: 63006 AN XY: 178682

Gnomad4 AFR exome AF: 0.383

Gnomad4 AMR exome AF: 0.323

Gnomad4 ASJ exome AF: 0.288

Gnomad4 EAS exome AF: 0.472

Gnomad4 SAS exome AF: 0.501

Gnomad4 FIN exome AF: 0.332

Gnomad4 NFE exome AF: 0.293

Gnomad4 OTH exome AF: 0.312

GnomAD4 genome AF: 0.354 AC: 53780 AN: 152020 Hom.: 9749 Cov.: 33 AF XY: 0.360 AC XY: 26770 AN XY: 74322

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.347

Alfa AF: 0.338 Hom.: 1115

Bravo AF: 0.351

Asia WGS AF: 0.557 AC: 1938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	2.8
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7074242; hg19: chr10-92814745;