rs12413153

Variant names:

• chr10-91055067-T-G
• rs12413153

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.119 in 371,842 control chromosomes in the GnomAD database, including 3,402 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 0.10 (1149 hom., cov: 33)
  • Exomes 𝑓: 0.13 (2253 hom.)
• Consequence: DDX18P6 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45
• Publications: 2 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DDX18P6		n.91055067T>G		intragenic_variant
LINC00502	NR_047467.2	n.360-6912T>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00502	ENST00000423621.2	n.815-6912T>G		intron_variant	Intron 7 of 7	3
ENSG00000273124	ENST00000607979.2	n.151-57239A>C		intron_variant	Intron 1 of 1	6
LINC00502	ENST00000846440.1	n.370-6912T>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15977 AN: 152116 Hom.: 1150 Cov.: 33

Gnomad AFR AF: 0.0431

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0990

Gnomad OTH AF: 0.124

GnomAD4 exome AF: 0.128 AC: 28135 AN: 219608 Hom.: 2253 Cov.: 0 AF XY: 0.126 AC XY: 15595 AN XY: 123430

African (AFR) AF: 0.0441 AC: 220 AN: 4984

American (AMR) AF: 0.271 AC: 3425 AN: 12654

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 664 AN: 4092

East Asian (EAS) AF: 0.312 AC: 2872 AN: 9218

South Asian (SAS) AF: 0.135 AC: 4486 AN: 33294

European-Finnish (FIN) AF: 0.107 AC: 2690 AN: 25112

Middle Eastern (MID) AF: 0.144 AC: 100 AN: 694

European-Non Finnish (NFE) AF: 0.104 AC: 12460 AN: 119794

Other (OTH) AF: 0.125 AC: 1218 AN: 9766

GnomAD4 genome AF: 0.105 AC: 15972 AN: 152234 Hom.: 1149 Cov.: 33 AF XY: 0.110 AC XY: 8165 AN XY: 74428

African (AFR) AF: 0.0430 AC: 1786 AN: 41558

American (AMR) AF: 0.207 AC: 3171 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3472

East Asian (EAS) AF: 0.305 AC: 1577 AN: 5166

South Asian (SAS) AF: 0.130 AC: 625 AN: 4826

European-Finnish (FIN) AF: 0.106 AC: 1124 AN: 10594

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0990 AC: 6735 AN: 68012

Other (OTH) AF: 0.123 AC: 260 AN: 2110

Alfa AF: 0.0931 Hom.: 231

Bravo AF: 0.113

Asia WGS AF: 0.189 AC: 656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.7
DANN	Benign	0.54
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs12413153; hg19: chr10-92814824;