rs4550218

Variant names:

• chr11-22842112-C-G
• rs4550218
• ENST00000499625.1:n.484+3748C>G

Variant summary

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

The ENST00000499625.1(ENSG00000246225):​n.484+3748C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 151,870 control chromosomes in the GnomAD database, including 12,053 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 0.39 (12053 hom., cov: 31)
• Consequence: ENSG00000246225 ENST00000499625.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 3 publications found

Genes affected

ENSG00000246225 (HGNC:):

LINC02718 (HGNC:54235): (long intergenic non-protein coding RNA 2718)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02718	NR_187205.1	n.492+3748C>G		intron_variant	Intron 3 of 13
LINC02718	NR_187206.1	n.492+3748C>G		intron_variant	Intron 3 of 11
LINC02718	NR_187207.1	n.492+3748C>G		intron_variant	Intron 3 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246225	ENST00000499625.1	n.484+3748C>G		intron_variant	Intron 3 of 4	5
ENSG00000246225	ENST00000525963.5	n.526+3748C>G		intron_variant	Intron 3 of 3	5
ENSG00000246225	ENST00000528701.6	n.494+3748C>G		intron_variant	Intron 3 of 3	4
ENSG00000246225	ENST00000661691.1	n.452+3748C>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59189 AN: 151752 Hom.: 12047 Cov.: 31

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.390 AC: 59226 AN: 151870 Hom.: 12053 Cov.: 31 AF XY: 0.392 AC XY: 29130 AN XY: 74230

African (AFR) AF: 0.406 AC: 16810 AN: 41392

American (AMR) AF: 0.441 AC: 6729 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1282 AN: 3470

East Asian (EAS) AF: 0.642 AC: 3315 AN: 5162

South Asian (SAS) AF: 0.564 AC: 2712 AN: 4812

European-Finnish (FIN) AF: 0.255 AC: 2682 AN: 10522

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24357 AN: 67954

Other (OTH) AF: 0.413 AC: 870 AN: 2108

Alfa AF: 0.359 Hom.: 1207

Bravo AF: 0.401

Asia WGS AF: 0.581 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.6
DANN	Benign	0.83
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs4550218; hg19: chr11-22863658;