rs10497691

Positions:

• 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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01090	ENST00000434418.2	n.496+93661C>T		intron_variant, non_coding_transcript_variant		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;