rs11334044

chr3-16526577-TAA-Tchr3-16526577-TAA-TAchr3-16526577-TAA-TAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000661221.1(LINC00690):n.553+1265_553+1266del 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 0.000136 in 147,062 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 ENST00000661221.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.458

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00690	ENST00000661221.1	n.553+1265_553+1266del		intron_variant, non_coding_transcript_variant
	ENST00000667160.1	n.176+490_176+491del		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0000498

Gnomad4 AMR AF: 0.000135

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000198

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000424

Gnomad4 NFE AF: 0.000166

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11334044; hg19: chr3-16568084;