20-23161018-T-C

Variant names:

• chr20-23161018-T-C
• rs844917
• XR_937371.2:n.229+1150T>C

Variant summary

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

The XR_937371.2(LINC03125):​n.229+1150T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,232 control chromosomes in the GnomAD database, including 53,262 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 0.84 (53219 hom., cov: 31)
  • Exomes 𝑓: 0.85 (43 hom.)
• Consequence: LINC03125 XR_937371.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329

Genes affected

LINC03125 (HGNC:57012):

RNA5SP478 (HGNC:43378): (RNA, 5S ribosomal pseudogene 478)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03125	XR_937371.2	n.229+1150T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNA5SP478	ENST00000364657.1	n.-47A>G		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126933 AN: 151994 Hom.: 53169 Cov.: 31

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.855

GnomAD4 exome AF: 0.850 AC: 102 AN: 120 Hom.: 43 Cov.: 0 AF XY: 0.857 AC XY: 72 AN XY: 84

Gnomad4 AFR exome AF: 0.750

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.844

Gnomad4 OTH exome AF: 0.875

GnomAD4 genome AF: 0.835 AC: 127043 AN: 152112 Hom.: 53219 Cov.: 31 AF XY: 0.833 AC XY: 61952 AN XY: 74346

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.856

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.887

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.857

Alfa AF: 0.835 Hom.: 73643

Bravo AF: 0.844

Asia WGS AF: 0.930 AC: 3232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs844917; hg19: chr20-23141655;