rs6876885

Variant names:

• chr5-17803161-T-G
• rs6876885
• ENST00000511596.5:n.195+34177T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000511596.5(LINC02223):​n.195+34177T>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02223	ENST00000511596.5	n.195+34177T>G		intron_variant	Intron 2 of 4	5
LINC02223	ENST00000514771.7	n.192+587T>G		intron_variant	Intron 1 of 6	5
LINC02223	ENST00000650405.1	n.217+59148T>G		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.486 AC: 20174 AN: 41478

American (AMR) AF: 0.341 AC: 5205 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1058 AN: 3468

East Asian (EAS) AF: 0.457 AC: 2358 AN: 5160

South Asian (SAS) AF: 0.338 AC: 1630 AN: 4822

European-Finnish (FIN) AF: 0.310 AC: 3277 AN: 10580

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20464 AN: 67968

Other (OTH) AF: 0.321 AC: 679 AN: 2116

Alfa AF: 0.313 Hom.: 8390

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
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs6876885; hg19: chr5-17803270;