rs10520945

chr5-28977395-A-T

Variant summary

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

The ENST00000658190.1(LINC02109):n.818+167247A>T 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 0.0222 in 152,250 control chromosomes in the GnomAD database, including 237 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 0.022 (237 hom., cov: 31)
• Consequence: LINC02109 ENST00000658190.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218

Genes affected

LINC02109 (HGNC:52964): (long intergenic non-protein coding RNA 2109)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02109	ENST00000658190.1	n.818+167247A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0221 AC: 3369 AN: 152132 Hom.: 231 Cov.: 31

Gnomad AFR AF: 0.00625

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.0370

Gnomad FIN AF: 0.00349

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00172

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0222 AC: 3387 AN: 152250 Hom.: 237 Cov.: 31 AF XY: 0.0251 AC XY: 1865 AN XY: 74448

Gnomad4 AFR AF: 0.00623

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.0370

Gnomad4 FIN AF: 0.00349

Gnomad4 NFE AF: 0.00172

Gnomad4 OTH AF: 0.0223

Alfa AF: 0.0113 Hom.: 13

Bravo AF: 0.0335

Asia WGS AF: 0.0830 AC: 286 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.71
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520945; hg19: chr5-28977502;