rs10469735

Variant names:

• chr2-188289788-T-C
• rs10469735
• ENST00000632331.1:n.80+94446A>G

Variant summary

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

The ENST00000632331.1(LINC01090):​n.80+94446A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,144 control chromosomes in the GnomAD database, including 2,002 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 0.16 (2002 hom., cov: 32)
• Consequence: LINC01090 ENST00000632331.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330

Genes affected

LINC01090 (HGNC:49201): (long intergenic non-protein coding RNA 1090)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01090	ENST00000632331.1	n.80+94446A>G		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23668 AN: 152026 Hom.: 1995 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0510

Gnomad SAS AF: 0.0731

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.156 AC: 23719 AN: 152144 Hom.: 2002 Cov.: 32 AF XY: 0.154 AC XY: 11448 AN XY: 74394

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.0511

Gnomad4 SAS AF: 0.0727

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.158

Alfa AF: 0.148 Hom.: 1572

Bravo AF: 0.154

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10469735; hg19: chr2-189154515;