rs893909

chr15-66636205-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.60-28157T>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 0.185 in 152,214 control chromosomes in the GnomAD database, including 2,787 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 0.19 (2787 hom., cov: 33)
• Consequence: LINC01169 NR_110372.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01169	NR_110372.1	n.60-28157T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01169	ENST00000558797.1	n.60-28157T>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28140 AN: 152096 Hom.: 2782 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.185 AC: 28163 AN: 152214 Hom.: 2787 Cov.: 33 AF XY: 0.182 AC XY: 13572 AN XY: 74418

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.174

Alfa AF: 0.194 Hom.: 357

Bravo AF: 0.183

Asia WGS AF: 0.229 AC: 794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.028
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs893909; hg19: chr15-66928543;