rs10484100

Variant names:

• chr14-86350752-A-G
• rs10484100
• ENST00000553679.1:n.133+14266A>G

Your query was ambiguous. Multiple possible variants found:

• chr14-86350752-A-G
• chr14-86350752-A-T

Variant summary

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

The ENST00000553679.1(LINC02309):​n.133+14266A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,198 control chromosomes in the GnomAD database, including 1,493 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 0.12 (1493 hom., cov: 32)
• Consequence: LINC02309 ENST00000553679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512
• Publications: 1 publications found

Genes affected

LINC02309 (HGNC:53228): (long intergenic non-protein coding RNA 2309)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553679.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02309	ENST00000553679.1	TSL:3	n.133+14266A>G		intron	N/A
	LINC02309	ENST00000730143.1		n.282-6742A>G		intron	N/A
	LINC02309	ENST00000730144.1		n.282-6742A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18826 AN: 152080 Hom.: 1495 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.0659

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0664

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0954

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.124 AC: 18849 AN: 152198 Hom.: 1493 Cov.: 32 AF XY: 0.121 AC XY: 8970 AN XY: 74414

African (AFR) AF: 0.219 AC: 9080 AN: 41506

American (AMR) AF: 0.0658 AC: 1006 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0867 AC: 301 AN: 3470

East Asian (EAS) AF: 0.0217 AC: 112 AN: 5168

South Asian (SAS) AF: 0.145 AC: 697 AN: 4822

European-Finnish (FIN) AF: 0.0664 AC: 704 AN: 10610

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0953 AC: 6484 AN: 68010

Other (OTH) AF: 0.119 AC: 251 AN: 2116

Alfa AF: 0.105 Hom.: 313

Bravo AF: 0.125

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.44
DANN	Benign	0.53
PhyloP100		-0.51
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10484100; hg19: chr14-86817096;