ENST00000569242.1:n.300+4679A>G

Variant names:

• chr16-35368509-A-G
• rs13332284
• ENST00000569242.1:n.300+4679A>G

Variant summary

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

The ENST00000569242.1(LINC01566):​n.300+4679A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0655 in 152,116 control chromosomes in the GnomAD database, including 1,002 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 0.066 (1002 hom., cov: 33)
• Consequence: LINC01566 ENST00000569242.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 3 publications found

Genes affected

LINC01566 (HGNC:27555): (long intergenic non-protein coding RNA 1566)

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 (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01566	NR_027079.2	n.300+4679A>G		intron_variant	Intron 1 of 8
LINC01566	NR_027080.2	n.113+4981A>G		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01566	ENST00000569242.1	n.300+4679A>G		intron_variant	Intron 1 of 8	1
LINC01566	ENST00000561756.6	n.117+4981A>G		intron_variant	Intron 1 of 4	3
LINC01566	ENST00000726698.1	n.277+4679A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0652 AC: 9914 AN: 151998 Hom.: 990 Cov.: 33

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0295

Gnomad ASJ AF: 0.0306

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00683

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00323

Gnomad OTH AF: 0.0417

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

GnomAD4 genome AF: 0.0655 AC: 9964 AN: 152116 Hom.: 1002 Cov.: 33 AF XY: 0.0640 AC XY: 4763 AN XY: 74386

African (AFR) AF: 0.218 AC: 9022 AN: 41438

American (AMR) AF: 0.0294 AC: 449 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0306 AC: 106 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.00663 AC: 32 AN: 4826

European-Finnish (FIN) AF: 0.0000942 AC: 1 AN: 10612

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00325 AC: 221 AN: 68018

Other (OTH) AF: 0.0413 AC: 87 AN: 2106

Alfa AF: 0.0209 Hom.: 46

Bravo AF: 0.0738

Asia WGS AF: 0.0150 AC: 52 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	0.37
DANN	Benign	0.48
PhyloP100		-0.83
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs13332284; hg19: chr16-34602880;