rs10517086

Variant names:

• chr4-26083889-G-A
• rs10517086
• ENST00000637313.1:n.1408+3299G>A

Variant summary

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

The ENST00000733074.1(LINC02357):​n.407+3299G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,032 control chromosomes in the GnomAD database, including 5,888 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 0.27 (5888 hom., cov: 32)
• Consequence: LINC02357 ENST00000733074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.948
• Publications: 82 publications found

Genes affected

LINC02357 (HGNC:53279): (long intergenic non-protein coding RNA 2357)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000733074.1. 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
	LINC02357	ENST00000637313.1	TSL:5	n.1408+3299G>A		intron	N/A
	LINC02357	ENST00000733074.1		n.407+3299G>A		intron	N/A
	LINC02357	ENST00000733075.1		n.371+3299G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.270 AC: 40955 AN: 151914 Hom.: 5878 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.270 AC: 40986 AN: 152032 Hom.: 5888 Cov.: 32 AF XY: 0.264 AC XY: 19630 AN XY: 74308

African (AFR) AF: 0.285 AC: 11810 AN: 41418

American (AMR) AF: 0.239 AC: 3660 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 923 AN: 3470

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5186

South Asian (SAS) AF: 0.135 AC: 653 AN: 4822

European-Finnish (FIN) AF: 0.273 AC: 2880 AN: 10568

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20095 AN: 67968

Other (OTH) AF: 0.280 AC: 591 AN: 2110

Alfa AF: 0.284 Hom.: 31171

Bravo AF: 0.270

Asia WGS AF: 0.0760 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	14
DANN	Benign	0.71
PhyloP100		0.95

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: rs10517086;

hg19: chr4-26085511;