rs2039945

chr13-24335614-G-C

Variant summary

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

The NR_131903.1(LINC00566):n.88-1025G>C 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 0.115 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 NR_131903.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC00566	NR_131903.1	n.88-1025G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00566	ENST00000561557.1	n.88-1025G>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0997

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0504

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.146

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2039945; hg19: chr13-24909752;