9-106154430-G-T

Variant names:

• chr9-106154430-G-T
• rs12686569
• ENST00000637185.1:n.559+160562G>T

Variant summary

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

The ENST00000637185.1(LINC01505):​n.559+160562G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,034 control chromosomes in the GnomAD database, including 6,991 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 0.30 (6991 hom., cov: 32)
• Consequence: LINC01505 ENST00000637185.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259
• Publications: 4 publications found

Genes affected

LINC01505 (HGNC:51186): (long intergenic non-protein coding RNA 1505)

LOC107987108 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637185.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01505	ENST00000637185.1	TSL:5	n.559+160562G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45655 AN: 151916 Hom.: 6979 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.301 AC: 45696 AN: 152034 Hom.: 6991 Cov.: 32 AF XY: 0.302 AC XY: 22407 AN XY: 74286

African (AFR) AF: 0.244 AC: 10113 AN: 41472

American (AMR) AF: 0.324 AC: 4945 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1139 AN: 3470

East Asian (EAS) AF: 0.435 AC: 2246 AN: 5164

South Asian (SAS) AF: 0.187 AC: 901 AN: 4810

European-Finnish (FIN) AF: 0.328 AC: 3456 AN: 10536

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21884 AN: 67990

Other (OTH) AF: 0.318 AC: 673 AN: 2114

Alfa AF: 0.314 Hom.: 6041

Bravo AF: 0.300

Asia WGS AF: 0.272 AC: 947 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.40
DANN	Benign	0.29
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs12686569; hg19: chr9-108916711;