3-16526577-TAA-TA

Variant names:

• chr3-16526577-TA-T
• rs11334044
• ENST00000655456.1:n.468+1255delA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000655456.1(LINC00690):​n.468+1255delA 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 0.33 (7749 hom., cov: 0)
• Consequence: LINC00690 ENST00000655456.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.363 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
LINC00690	ENST00000655456.1	n.468+1255delA		intron_variant	Intron 1 of 4
LINC00690	ENST00000659804.1	n.543+1255delA		intron_variant	Intron 1 of 2
LINC00690	ENST00000660552.1	n.500+1255delA		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.326 AC: 47898 AN: 146772 Hom.: 7732 Cov.: 0

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.327 AC: 47962 AN: 146864 Hom.: 7749 Cov.: 0 AF XY: 0.331 AC XY: 23671 AN XY: 71464

African (AFR) AF: 0.350 AC: 14025 AN: 40126

American (AMR) AF: 0.371 AC: 5497 AN: 14808

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 777 AN: 3388

East Asian (EAS) AF: 0.346 AC: 1748 AN: 5048

South Asian (SAS) AF: 0.334 AC: 1547 AN: 4630

European-Finnish (FIN) AF: 0.377 AC: 3544 AN: 9408

Middle Eastern (MID) AF: 0.286 AC: 80 AN: 280

European-Non Finnish (NFE) AF: 0.298 AC: 19753 AN: 66248

Other (OTH) AF: 0.321 AC: 650 AN: 2026

Alfa AF: 0.161 Hom.: 303

Bravo AF: 0.318

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.14

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;