rs2090409

Variant names:

• chr9-106204807-C-A
• rs2090409
• ENST00000637185.1:n.559+210939C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-106204807-C-A
• chr9-106204807-C-G
• chr9-106204807-C-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+210939C>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188
• Publications: 40 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=-0.99).
• 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 rank	MANE	Protein	UniProt
LOC107987108	XR_001746870.2	n.2032+228676C>A		intron_variant	Intron 3 of 5
LOC107987108	XR_007061713.1	n.2032+228676C>A		intron_variant	Intron 3 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01505	ENST00000637185.1	n.559+210939C>A		intron_variant	Intron 1 of 7	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

African (AFR) AF: 0.380 AC: 15653 AN: 41234

American (AMR) AF: 0.335 AC: 5097 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1143 AN: 3472

East Asian (EAS) AF: 0.435 AC: 2233 AN: 5132

South Asian (SAS) AF: 0.183 AC: 880 AN: 4806

European-Finnish (FIN) AF: 0.329 AC: 3456 AN: 10498

Middle Eastern (MID) AF: 0.341 AC: 99 AN: 290

European-Non Finnish (NFE) AF: 0.322 AC: 21863 AN: 67934

Other (OTH) AF: 0.346 AC: 727 AN: 2104

Alfa AF: 0.328 Hom.: 26690

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
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs2090409; hg19: chr9-108967088;