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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720785.1. 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
	LINC02498	ENST00000720785.1		n.192-4661G>A		intron	N/A
	LINC02498	ENST00000720792.1		n.422+19575G>A		intron	N/A
	LINC02498	ENST00000720793.1		n.324-4661G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10516211;

hg19: chr4-10756057;