rs11334044

Variant names:

• chr3-16526577-TAA-T
• rs11334044
• ENST00000655456.1:n.468+1255_468+1256delAA

Your query was ambiguous. Multiple possible variants found:

• chr3-16526577-TAA-T
• chr3-16526577-TAA-TA
• chr3-16526577-TAA-TAAA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000655456.1(LINC00690):​n.468+1255_468+1256delAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.00014 (0 hom., cov: 0)
• Consequence: LINC00690 ENST00000655456.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.458
• Publications: 1 publications found

Genes affected

LINC00690 (HGNC:44503): (long intergenic non-protein coding RNA 690)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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
LINC00690	ENST00000655456.1	n.468+1255_468+1256delAA		intron_variant	Intron 1 of 4
LINC00690	ENST00000659804.1	n.543+1255_543+1256delAA		intron_variant	Intron 1 of 2
LINC00690	ENST00000660552.1	n.500+1255_500+1256delAA		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.000136 AC: 20 AN: 146970 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000499

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000135

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000197

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000424

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000166

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.000136 AC: 20 AN: 147062 Hom.: 0 Cov.: 0 AF XY: 0.000140 AC XY: 10 AN XY: 71580

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000498 AC: 2 AN: 40170

American (AMR) AF: 0.000135 AC: 2 AN: 14822

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3400

East Asian (EAS) AF: 0.000198 AC: 1 AN: 5058

South Asian (SAS) AF: 0.00 AC: 0 AN: 4634

European-Finnish (FIN) AF: 0.000424 AC: 4 AN: 9428

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 280

European-Non Finnish (NFE) AF: 0.000166 AC: 11 AN: 66332

Other (OTH) AF: 0.00 AC: 0 AN: 2034

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000079), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 303

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs11334044; hg19: chr3-16568084;