rs2039945

Variant names:

• chr13-24335614-G-C
• rs2039945
• ENST00000561557.2:n.88-1025G>C

Variant summary

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

The ENST00000561557.2(LINC00566):​n.88-1025G>C 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 152,282 control chromosomes in the GnomAD database, including 1,143 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 (1143 hom., cov: 32)
• Consequence: LINC00566 ENST00000561557.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 3 publications found

Genes affected

LINC00566 (HGNC:43710): (long intergenic non-protein coding RNA 566)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00566	NR_131903.1	n.88-1025G>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00566	ENST00000561557.2	n.88-1025G>C		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17547 AN: 152164 Hom.: 1144 Cov.: 32

Gnomad AFR AF: 0.0998

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0504

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.115 AC: 17549 AN: 152282 Hom.: 1143 Cov.: 32 AF XY: 0.112 AC XY: 8376 AN XY: 74462

African (AFR) AF: 0.0997 AC: 4144 AN: 41562

American (AMR) AF: 0.104 AC: 1592 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 688 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5186

South Asian (SAS) AF: 0.0504 AC: 243 AN: 4822

European-Finnish (FIN) AF: 0.130 AC: 1378 AN: 10610

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9025 AN: 68006

Other (OTH) AF: 0.146 AC: 309 AN: 2112

Alfa AF: 0.113 Hom.: 140

Bravo AF: 0.116

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.011
DANN	Benign	0.49
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2039945; hg19: chr13-24909752;