chr9-106522886-G-A

Variant names:

• chr9-106522886-G-A
• rs6477526
• ENST00000425709.3:n.171-35586G>A

Variant summary

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

The ENST00000425709.3(LINC01505):​n.171-35586G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,044 control chromosomes in the GnomAD database, including 3,958 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 0.21 (3958 hom., cov: 32)
• Consequence: LINC01505 ENST00000425709.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 1 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425709.3. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01505	ENST00000425709.3	TSL:1	n.171-35586G>A		intron	N/A
	LINC01505	ENST00000411451.3	TSL:3	n.75-35586G>A		intron	N/A
	LINC01505	ENST00000435485.5	TSL:5	n.446+22381G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32375 AN: 151926 Hom.: 3941 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.0761

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.213 AC: 32435 AN: 152044 Hom.: 3958 Cov.: 32 AF XY: 0.215 AC XY: 15991 AN XY: 74314

African (AFR) AF: 0.319 AC: 13230 AN: 41464

American (AMR) AF: 0.215 AC: 3283 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0761 AC: 264 AN: 3470

East Asian (EAS) AF: 0.254 AC: 1307 AN: 5152

South Asian (SAS) AF: 0.245 AC: 1180 AN: 4822

European-Finnish (FIN) AF: 0.219 AC: 2307 AN: 10558

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10345 AN: 67980

Other (OTH) AF: 0.188 AC: 397 AN: 2116

Alfa AF: 0.194 Hom.: 362

Bravo AF: 0.217

Asia WGS AF: 0.263 AC: 918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.87
DANN	Benign	0.40
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs6477526; hg19: chr9-109285167;