rs4562969

Positions:

• chr14-106520947-C-A
• chr14-106520947-C-T

Variant summary

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

The ENST00000619530.1(LINC00221):​n.1373C>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 0.61 in 151,554 control chromosomes in the GnomAD database, including 28,803 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 0.61 (28803 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC00221 ENST00000619530.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173

Genes affected

LINC00221 (HGNC:20169): (long intergenic non-protein coding RNA 221)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=4.062).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00221	ENST00000619530.1	n.1373C>A		non_coding_transcript_exon_variant	4/4	2

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92315 AN: 151440 Hom.: 28777 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.638

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.610 AC: 92376 AN: 151554 Hom.: 28803 Cov.: 32 AF XY: 0.602 AC XY: 44529 AN XY: 74012

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.639

Alfa AF: 0.704 Hom.: 6712

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	4.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4562969; hg19: -;