rs2468475

Variant names:

• chr5-28299109-G-A
• rs2468475
• ENST00000747433.1:n.77+1910C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-28299109-G-A
• chr5-28299109-G-C
• chr5-28299109-G-T

Variant summary

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

The ENST00000747433.1(LINC02103):​n.77+1910C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 151,882 control chromosomes in the GnomAD database, including 13,929 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 0.42 (13929 hom., cov: 32)
• Consequence: LINC02103 ENST00000747433.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.835
• Publications: 2 publications found

Genes affected

LINC02103 (HGNC:52958): (long intergenic non-protein coding RNA 2103)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747433.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02103	ENST00000747433.1		n.77+1910C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64043 AN: 151766 Hom.: 13916 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.422 AC: 64086 AN: 151882 Hom.: 13929 Cov.: 32 AF XY: 0.420 AC XY: 31177 AN XY: 74208

African (AFR) AF: 0.353 AC: 14634 AN: 41432

American (AMR) AF: 0.396 AC: 6041 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1638 AN: 3470

East Asian (EAS) AF: 0.195 AC: 1002 AN: 5146

South Asian (SAS) AF: 0.339 AC: 1629 AN: 4806

European-Finnish (FIN) AF: 0.485 AC: 5107 AN: 10536

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.477 AC: 32398 AN: 67912

Other (OTH) AF: 0.460 AC: 971 AN: 2110

Alfa AF: 0.447 Hom.: 14692

Bravo AF: 0.413

Asia WGS AF: 0.282 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.6
DANN	Benign	0.35
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs2468475; hg19: chr5-28299216;