rs2062140

Positions:

• chr5-44496313-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_131946.1(LINC02224):​n.451-520C>T 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 0.0663 in 152,134 control chromosomes in the GnomAD database, including 409 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 0.066 (409 hom., cov: 32)
• Consequence: LINC02224 NR_131946.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.674

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02224	NR_131946.1	n.451-520C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02224	ENST00000671607.1	n.400-520C>T		intron_variant, non_coding_transcript_variant
LINC02224	ENST00000505706.1	n.409-520C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0663 AC: 10081 AN: 152016 Hom.: 408 Cov.: 32

Gnomad AFR AF: 0.0736

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0660

Gnomad ASJ AF: 0.0749

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0205

Gnomad FIN AF: 0.0558

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.0714

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0663 AC: 10087 AN: 152134 Hom.: 409 Cov.: 32 AF XY: 0.0650 AC XY: 4837 AN XY: 74394

Gnomad4 AFR AF: 0.0736

Gnomad4 AMR AF: 0.0659

Gnomad4 ASJ AF: 0.0749

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0205

Gnomad4 FIN AF: 0.0558

Gnomad4 NFE AF: 0.0714

Gnomad4 OTH AF: 0.0676

Alfa AF: 0.0709 Hom.: 540

Bravo AF: 0.0673

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	-0.44
CADD	Benign	16
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2062140; hg19: chr5-44496415;