rs990324

Variant names:

• chr13-32813108-A-G
• rs990324
• NR_047020.1:n.906-3468T>C

Variant summary

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

The NR_047020.1(LINC00423):​n.906-3468T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,184 control chromosomes in the GnomAD database, including 4,646 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 0.19 (4646 hom., cov: 33)
• Consequence: LINC00423 NR_047020.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340
• Publications: 9 publications found

Genes affected

LINC00423 (HGNC:42758): (long intergenic non-protein coding RNA 423)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00423	NR_047020.1	n.906-3468T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28411 AN: 152064 Hom.: 4621 Cov.: 33

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0215

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0643

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.0861

Gnomad OTH AF: 0.154

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.187 AC: 28481 AN: 152184 Hom.: 4646 Cov.: 33 AF XY: 0.184 AC XY: 13727 AN XY: 74426

African (AFR) AF: 0.448 AC: 18587 AN: 41464

American (AMR) AF: 0.110 AC: 1676 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 463 AN: 3472

East Asian (EAS) AF: 0.0216 AC: 112 AN: 5194

South Asian (SAS) AF: 0.131 AC: 631 AN: 4824

European-Finnish (FIN) AF: 0.0643 AC: 682 AN: 10612

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.0860 AC: 5851 AN: 68006

Other (OTH) AF: 0.155 AC: 327 AN: 2112

Alfa AF: 0.123 Hom.: 7330

Bravo AF: 0.205

Asia WGS AF: 0.110 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.71
DANN	Benign	0.28
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs990324; hg19: chr13-33387246;