15-66598566-T-A

Position:

• chr15-66598566-T-A

Variant summary

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

The NR_110372.1(LINC01169):​n.59+16318T>A 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 0.0856 in 152,190 control chromosomes in the GnomAD database, including 794 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 0.086 (794 hom., cov: 32)
• Consequence: LINC01169 NR_110372.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

Genes affected

LINC01169 (HGNC:49541): (long intergenic non-protein coding RNA 1169)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01169	NR_110372.1	n.59+16318T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01169	ENST00000558797.1	n.59+16318T>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0857 AC: 13034 AN: 152072 Hom.: 795 Cov.: 32

Gnomad AFR AF: 0.0636

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0656

Gnomad OTH AF: 0.0943

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

GnomAD4 genome AF: 0.0856 AC: 13025 AN: 152190 Hom.: 794 Cov.: 32 AF XY: 0.0891 AC XY: 6627 AN XY: 74390

Gnomad4 AFR AF: 0.0634

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.0535

Gnomad4 NFE AF: 0.0656

Gnomad4 OTH AF: 0.0942

Alfa AF: 0.0743 Hom.: 62

Bravo AF: 0.0934

Asia WGS AF: 0.229 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.55
DANN	Benign	0.65
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16950046; hg19: chr15-66890904;