rs10503857

Variant names:

• chr8-29932192-A-G
• rs10503857
• ENST00000521245.2:n.1411+8871A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-29932192-A-G
• chr8-29932192-A-T

Variant summary

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

The ENST00000521245.2(LINC02209):​n.1411+8871A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0614 in 152,214 control chromosomes in the GnomAD database, including 398 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 0.061 (398 hom., cov: 32)
• Consequence: LINC02209 ENST00000521245.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679
• Publications: 2 publications found

Genes affected

LINC02209 (HGNC:27827): (long intergenic non-protein coding RNA 2209)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02209	NR_024473.1	n.1422+8871A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02209	ENST00000521245.2	n.1411+8871A>G		intron_variant	Intron 2 of 2	1
LINC02209	ENST00000524059.5	n.1422+8871A>G		intron_variant	Intron 2 of 2	1
LINC02209	ENST00000657328.1	n.336+8871A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0613 AC: 9330 AN: 152096 Hom.: 398 Cov.: 32

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0528

Gnomad ASJ AF: 0.0518

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.0604

Gnomad FIN AF: 0.0598

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0553

Gnomad OTH AF: 0.0690

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

GnomAD4 genome AF: 0.0614 AC: 9350 AN: 152214 Hom.: 398 Cov.: 32 AF XY: 0.0620 AC XY: 4616 AN XY: 74400

African (AFR) AF: 0.0536 AC: 2225 AN: 41546

American (AMR) AF: 0.0528 AC: 807 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0518 AC: 180 AN: 3472

East Asian (EAS) AF: 0.242 AC: 1252 AN: 5166

South Asian (SAS) AF: 0.0607 AC: 293 AN: 4830

European-Finnish (FIN) AF: 0.0598 AC: 634 AN: 10596

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0553 AC: 3764 AN: 68004

Other (OTH) AF: 0.0707 AC: 149 AN: 2108

Alfa AF: 0.0238 Hom.: 9

Bravo AF: 0.0603

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.64
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs10503857; hg19: chr8-29789708;