rs3852494

Variant names:

• chr10-91051639-G-A
• rs3852494
• ENST00000423621.2:n.814+3610G>A

Variant summary

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

The ENST00000423621.2(LINC00502):​n.814+3610G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,212 control chromosomes in the GnomAD database, including 3,567 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 0.16 (3567 hom., cov: 32)
• Consequence: LINC00502 ENST00000423621.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45
• Publications: 1 publications found

Genes affected

LINC00502 (HGNC:43442): (long intergenic non-protein coding RNA 502)

ENSG00000273124 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000423621.2. 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
	LINC00502	NR_047467.2		n.359+3610G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00502	ENST00000423621.2	TSL:3	n.814+3610G>A		intron	N/A
	ENSG00000273124	ENST00000607979.2	TSL:6	n.151-53811C>T		intron	N/A
	LINC00502	ENST00000846440.1		n.369+3610G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24180 AN: 152094 Hom.: 3542 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0707

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.0109

Gnomad SAS AF: 0.0493

Gnomad FIN AF: 0.0737

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0780

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.159 AC: 24245 AN: 152212 Hom.: 3567 Cov.: 32 AF XY: 0.154 AC XY: 11476 AN XY: 74430

African (AFR) AF: 0.394 AC: 16358 AN: 41484

American (AMR) AF: 0.0705 AC: 1078 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0343 AC: 119 AN: 3470

East Asian (EAS) AF: 0.0110 AC: 57 AN: 5194

South Asian (SAS) AF: 0.0485 AC: 234 AN: 4826

European-Finnish (FIN) AF: 0.0737 AC: 782 AN: 10608

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0780 AC: 5307 AN: 68022

Other (OTH) AF: 0.118 AC: 250 AN: 2110

Alfa AF: 0.134 Hom.: 324

Bravo AF: 0.169

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	8.3
DANN	Benign	0.55
PhyloP100		1.5

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: rs3852494;

hg19: chr10-92811396;