rs7074242

Variant names:

• chr10-91054988-G-A
• rs7074242
• ENST00000450119.1:n.1938G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.63).
• 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 rank	MANE	Protein	UniProt
DDX18P6		n.91054988G>A		intragenic_variant
LINC00502	NR_047467.2	n.359+6959G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DDX18P6	ENST00000450119.1	n.1938G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC00502	ENST00000423621.2	n.814+6959G>A		intron_variant	Intron 7 of 7	3
ENSG00000273124	ENST00000607979.2	n.151-57160C>T		intron_variant	Intron 1 of 1	6

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

African (AFR) AF: 0.383 AC: 2878 AN: 7506

American (AMR) AF: 0.323 AC: 7519 AN: 23310

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 2248 AN: 7806

East Asian (EAS) AF: 0.472 AC: 5701 AN: 12078

South Asian (SAS) AF: 0.501 AC: 25388 AN: 50654

European-Finnish (FIN) AF: 0.332 AC: 9624 AN: 29022

Middle Eastern (MID) AF: 0.284 AC: 327 AN: 1150

European-Non Finnish (NFE) AF: 0.293 AC: 48798 AN: 166626

Other (OTH) AF: 0.312 AC: 4298 AN: 13784

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

African (AFR) AF: 0.400 AC: 16600 AN: 41452

American (AMR) AF: 0.348 AC: 5322 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1118 AN: 3468

East Asian (EAS) AF: 0.478 AC: 2474 AN: 5172

South Asian (SAS) AF: 0.538 AC: 2593 AN: 4818

European-Finnish (FIN) AF: 0.336 AC: 3548 AN: 10570

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 20996 AN: 67948

Other (OTH) AF: 0.347 AC: 730 AN: 2104

Alfa AF: 0.340 Hom.: 1170

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
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs7074242; hg19: chr10-92814745;