rs6876885

chr5-17803161-T-G

Variant summary

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

The ENST00000511596.5(LINC02223):n.195+34177T>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 0.363 in 152,056 control chromosomes in the GnomAD database, including 10,603 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 0.36 (10603 hom., cov: 33)
• Consequence: LINC02223 ENST00000511596.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436

Genes affected

LINC02223 (HGNC:53092): (long intergenic non-protein coding RNA 2223)

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 (AFR) allele frequency at 95% confidence interval = 0.481 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
LINC02223	ENST00000511596.5	n.195+34177T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55196 AN: 151940 Hom.: 10581 Cov.: 33

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.363 AC: 55267 AN: 152056 Hom.: 10603 Cov.: 33 AF XY: 0.363 AC XY: 26968 AN XY: 74338

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.321

Alfa AF: 0.312 Hom.: 6989

Bravo AF: 0.372

Asia WGS AF: 0.425 AC: 1478 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	0.52
Dann	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6876885; hg19: chr5-17803270;