rs10516211

Variant names:

• chr4-10754433-G-A
• rs10516211
• ENST00000720785.1:n.192-4661G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-10754433-G-A
• chr4-10754433-G-T

Variant summary

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

The ENST00000720785.1(LINC02498):​n.192-4661G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 151,944 control chromosomes in the GnomAD database, including 7,143 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 0.29 (7143 hom., cov: 32)
• Consequence: LINC02498 ENST00000720785.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 3 publications found

Genes affected

LINC02498 (HGNC:53483): (long intergenic non-protein coding RNA 2498)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02498	XR_925377.3	n.632-4661G>A		intron_variant	Intron 2 of 3
LINC02498	XR_925378.3	n.632-4661G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02498	ENST00000720785.1	n.192-4661G>A		intron_variant	Intron 1 of 3
LINC02498	ENST00000720792.1	n.422+19575G>A		intron_variant	Intron 2 of 2
LINC02498	ENST00000720793.1	n.324-4661G>A		intron_variant	Intron 2 of 2
LINC02498	ENST00000720795.1	n.299-4661G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44381 AN: 151826 Hom.: 7114 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.292 AC: 44442 AN: 151944 Hom.: 7143 Cov.: 32 AF XY: 0.293 AC XY: 21761 AN XY: 74216

African (AFR) AF: 0.435 AC: 18016 AN: 41390

American (AMR) AF: 0.211 AC: 3218 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 742 AN: 3468

East Asian (EAS) AF: 0.280 AC: 1451 AN: 5180

South Asian (SAS) AF: 0.282 AC: 1356 AN: 4808

European-Finnish (FIN) AF: 0.295 AC: 3106 AN: 10532

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15664 AN: 67994

Other (OTH) AF: 0.299 AC: 630 AN: 2106

Alfa AF: 0.255 Hom.: 876

Bravo AF: 0.290

Asia WGS AF: 0.304 AC: 1057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.035
DANN	Benign	0.18
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10516211; hg19: chr4-10756057;