ENST00000413124.3:n.122+903A>G

Variant names:

• chr13-21877232-T-C
• rs765244
• ENST00000413124.3:n.122+903A>G

Variant summary

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

The ENST00000413124.3(LINC00424):​n.122+903A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,066 control chromosomes in the GnomAD database, including 4,829 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 0.25 (4829 hom., cov: 32)
• Consequence: LINC00424 ENST00000413124.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360

Genes affected

LINC00424 (HGNC:42815): (long intergenic non-protein coding RNA 424)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00424	NR_047040.1	n.26+903A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00424	ENST00000413124.3	n.122+903A>G		intron_variant	Intron 1 of 2	4
LINC00424	ENST00000624644.1	n.26+903A>G		intron_variant	Intron 1 of 1	3
LINC00424	ENST00000669854.1	n.122+903A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37913 AN: 151946 Hom.: 4829 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.249 AC: 37929 AN: 152066 Hom.: 4829 Cov.: 32 AF XY: 0.246 AC XY: 18276 AN XY: 74314

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.250

Alfa AF: 0.273 Hom.: 11920

Bravo AF: 0.249

Asia WGS AF: 0.267 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs765244; hg19: chr13-22451371;