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. The variant received -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
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434418.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01090	ENST00000434418.2	TSL:5	n.496+93661C>T		intron	N/A

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

African (AFR) AF: 0.122 AC: 5039 AN: 41468

American (AMR) AF: 0.134 AC: 2045 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0993 AC: 344 AN: 3464

East Asian (EAS) AF: 0.424 AC: 2185 AN: 5154

South Asian (SAS) AF: 0.173 AC: 835 AN: 4816

European-Finnish (FIN) AF: 0.151 AC: 1588 AN: 10536

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0950 AC: 6455 AN: 67976

Other (OTH) AF: 0.127 AC: 268 AN: 2104

Alfa AF: 0.104 Hom.: 1824

Bravo AF: 0.126

Asia WGS AF: 0.267 AC: 927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.4
DANN	Benign	0.63
PhyloP100		0.45

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10497691;

hg19: chr2-188806662;