rs16901892

Positions:

• chr5-44512967-T-C

Variant summary

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

The ENST00000671607.1(LINC02224):​n.109-8495A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0631 in 152,116 control chromosomes in the GnomAD database, including 368 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 0.063 (368 hom., cov: 32)
• Consequence: LINC02224 ENST00000671607.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

Genes affected

LINC02224 (HGNC:53093): (long intergenic non-protein coding RNA 2224)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.07 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02224	ENST00000671607.1	n.109-8495A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0631 AC: 9589 AN: 151998 Hom.: 367 Cov.: 32

Gnomad AFR AF: 0.0612

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0660

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.0559

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0716

Gnomad OTH AF: 0.0689

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

GnomAD4 genome AF: 0.0631 AC: 9596 AN: 152116 Hom.: 368 Cov.: 32 AF XY: 0.0622 AC XY: 4622 AN XY: 74364

Gnomad4 AFR AF: 0.0612

Gnomad4 AMR AF: 0.0659

Gnomad4 ASJ AF: 0.0767

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0203

Gnomad4 FIN AF: 0.0559

Gnomad4 NFE AF: 0.0717

Gnomad4 OTH AF: 0.0677

Alfa AF: 0.0674 Hom.: 202

Bravo AF: 0.0633

Asia WGS AF: 0.0160 AC: 56 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16901892; hg19: chr5-44513069;