rs10484100

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000553679.1(LINC02309):​n.133+14266A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02309	XR_944113.3	n.290-6742A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02309	ENST00000553679.1	n.133+14266A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.0658

Gnomad4 ASJ AF: 0.0867

Gnomad4 EAS AF: 0.0217

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.0664

Gnomad4 NFE AF: 0.0953

Gnomad4 OTH AF: 0.119

Alfa AF: 0.110 Hom.: 146

Bravo AF: 0.125

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.44
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484100; hg19: chr14-86817096;