rs2090409

Positions:

• chr9-106204807-C-A
• chr9-106204807-C-G
• chr9-106204807-C-T

Variant summary

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

The ENST00000637185.1(LINC01505):​n.559+210939C>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 0.339 in 151,606 control chromosomes in the GnomAD database, including 8,917 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 0.34 (8917 hom., cov: 31)
• Consequence: LINC01505 ENST00000637185.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987108	XR_007061713.1	n.2032+228676C>A		intron_variant, non_coding_transcript_variant
LOC107987108	XR_001746870.2	n.2032+228676C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01505	ENST00000637185.1	n.559+210939C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51311 AN: 151486 Hom.: 8883 Cov.: 31

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.327

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.339 AC: 51390 AN: 151606 Hom.: 8917 Cov.: 31 AF XY: 0.339 AC XY: 25116 AN XY: 74092

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.346

Alfa AF: 0.323 Hom.: 10438

Bravo AF: 0.344

Asia WGS AF: 0.282 AC: 982 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.36
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2090409; hg19: chr9-108967088;