9-106522886-G-A

Position:

• chr9-106522886-G-A

Variant summary

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

The ENST00000425709.2(LINC01505):​n.74-35586G>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 0.213 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 ENST00000425709.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

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

LOC107987108 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987108	XR_007061713.1	n.2307+22381G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01505	ENST00000637185.1	n.560-35586G>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.0761

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.188

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6477526; hg19: chr9-109285167;