rs10516583

Variant names:

• chr4-112104108-C-A
• rs10516583
• ENST00000679735.2:n.85+8081G>T

Variant summary

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

The ENST00000679735.2(LINC02945):​n.85+8081G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,058 control chromosomes in the GnomAD database, including 1,049 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 (1049 hom., cov: 31)
• Consequence: LINC02945 ENST00000679735.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.61
• Publications: 3 publications found

Genes affected

LINC02945 (HGNC:55960): (long intergenic non-protein coding RNA 2945)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02945	NR_186681.1	n.82+8081G>T		intron_variant	Intron 1 of 3
LINC02945	NR_186682.1	n.82+8081G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02945	ENST00000679735.2	n.85+8081G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17522 AN: 151940 Hom.: 1048 Cov.: 31

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0833

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0911

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.115 AC: 17537 AN: 152058 Hom.: 1049 Cov.: 31 AF XY: 0.117 AC XY: 8721 AN XY: 74314

African (AFR) AF: 0.142 AC: 5876 AN: 41474

American (AMR) AF: 0.143 AC: 2192 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0833 AC: 289 AN: 3468

East Asian (EAS) AF: 0.110 AC: 567 AN: 5164

South Asian (SAS) AF: 0.147 AC: 708 AN: 4818

European-Finnish (FIN) AF: 0.124 AC: 1308 AN: 10578

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0911 AC: 6189 AN: 67964

Other (OTH) AF: 0.117 AC: 246 AN: 2106

Alfa AF: 0.100 Hom.: 1402

Bravo AF: 0.118

Asia WGS AF: 0.115 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.021
DANN	Benign	0.70
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs10516583; hg19: chr4-113025264;