rs10520945

Variant names:

• chr5-28977395-A-T
• rs10520945
• ENST00000658190.1:n.818+167247A>T

Variant summary

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

The ENST00000658190.1(LINC02109):​n.818+167247A>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02109	ENST00000658190.1	n.818+167247A>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.00623 AC: 259 AN: 41568

American (AMR) AF: 0.121 AC: 1847 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3470

East Asian (EAS) AF: 0.159 AC: 823 AN: 5162

South Asian (SAS) AF: 0.0370 AC: 179 AN: 4834

European-Finnish (FIN) AF: 0.00349 AC: 37 AN: 10606

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00172 AC: 117 AN: 67998

Other (OTH) AF: 0.0223 AC: 47 AN: 2112

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
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs10520945; hg19: chr5-28977502;