rs13332284

Positions:

• chr16-35368509-A-G
• chr16-35368509-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC01566 (HGNC:):

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01566	NR_027079.2	n.300+4679A>G		intron_variant
LINC01566	NR_027080.2	n.113+4981A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01566	ENST00000569242.1	n.300+4679A>G		intron_variant		1
LINC01566	ENST00000561756.5	n.117+4981A>G		intron_variant		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

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.0294

Gnomad4 ASJ AF: 0.0306

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00663

Gnomad4 FIN AF: 0.0000942

Gnomad4 NFE AF: 0.00325

Gnomad4 OTH AF: 0.0413

Alfa AF: 0.0117 Hom.: 20

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13332284; hg19: chr16-34602880;