rs10497691

Variant names:

• chr2-187941935-G-A
• rs10497691
• ENST00000434418.2:n.496+93661C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-187941935-G-A
• chr2-187941935-G-T

Variant summary

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

The ENST00000434418.2(LINC01090):​n.496+93661C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,006 control chromosomes in the GnomAD database, including 1,521 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 0.12 (1521 hom., cov: 32)
• Consequence: LINC01090 ENST00000434418.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.447

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 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	ENST00000434418.2	n.496+93661C>T		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18823 AN: 151888 Hom.: 1520 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0993

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0949

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.124 AC: 18832 AN: 152006 Hom.: 1521 Cov.: 32 AF XY: 0.127 AC XY: 9432 AN XY: 74288

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.0993

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.0950

Gnomad4 OTH AF: 0.127

Alfa AF: 0.103 Hom.: 1324

Bravo AF: 0.126

Asia WGS AF: 0.267 AC: 927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497691; hg19: chr2-188806662;