rs893909

Variant names:

• chr15-66636205-T-A
• rs893909
• ENST00000558797.1:n.60-28157T>A

Variant summary

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

The ENST00000558797.1(LINC01169):​n.60-28157T>A variant causes a intron 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 ENST00000558797.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558797.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01169	NR_110372.1		n.60-28157T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01169	ENST00000558797.1	TSL:1	n.60-28157T>A		intron	N/A

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

African (AFR) AF: 0.229 AC: 9503 AN: 41528

American (AMR) AF: 0.131 AC: 2001 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3472

East Asian (EAS) AF: 0.192 AC: 996 AN: 5178

South Asian (SAS) AF: 0.231 AC: 1113 AN: 4828

European-Finnish (FIN) AF: 0.122 AC: 1294 AN: 10598

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12241 AN: 67990

Other (OTH) AF: 0.174 AC: 368 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.028
DANN	Benign	0.38
PhyloP100		-1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs893909;

hg19: chr15-66928543;