chr9-106620080-G-A

Position:

• chr9-106620080-G-A

Variant summary

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

The NR_104145.1(LINC01505):​n.259+3764G>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 0.151 in 152,194 control chromosomes in the GnomAD database, including 2,448 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 0.15 (2448 hom., cov: 33)
• Consequence: LINC01505 NR_104145.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01505	NR_104145.1	n.259+3764G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01505	ENST00000637185.1	n.760-18079G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22899 AN: 152076 Hom.: 2439 Cov.: 33

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.0736

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0268

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.0575

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0964

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.151 AC: 22941 AN: 152194 Hom.: 2448 Cov.: 33 AF XY: 0.151 AC XY: 11259 AN XY: 74424

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.0734

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.0267

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.0575

Gnomad4 NFE AF: 0.0964

Gnomad4 OTH AF: 0.135

Alfa AF: 0.120 Hom.: 826

Bravo AF: 0.151

Asia WGS AF: 0.192 AC: 668 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.7
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9942977; hg19: chr9-109382361;