rs1951033

Variant names:

• chr14-100668981-T-C
• rs1951033
• ENST00000360899.3:n.467-2580T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000360899.3(LINC00523):​n.467-2580T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.865 in 152,240 control chromosomes in the GnomAD database, including 58,465 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 0.87 (58465 hom., cov: 32)
• Consequence: LINC00523 ENST00000360899.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998
• Publications: 4 publications found

Genes affected

LINC00523 (HGNC:20117): (long intergenic non-protein coding RNA 523)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000360899.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00523	NR_024096.1		n.444-2580T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00523	ENST00000360899.3	TSL:1	n.467-2580T>C		intron	N/A
	LINC00523	ENST00000556308.1	TSL:4	n.348-340T>C		intron	N/A
	LINC00523	ENST00000556697.1	TSL:2	n.857-2580T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.865 AC: 131624 AN: 152122 Hom.: 58429 Cov.: 32

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.886

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

GnomAD4 genome AF: 0.865 AC: 131701 AN: 152240 Hom.: 58465 Cov.: 32 AF XY: 0.859 AC XY: 63928 AN XY: 74434

African (AFR) AF: 0.754 AC: 31306 AN: 41514

American (AMR) AF: 0.731 AC: 11183 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 3432 AN: 3472

East Asian (EAS) AF: 0.450 AC: 2328 AN: 5168

South Asian (SAS) AF: 0.922 AC: 4448 AN: 4826

European-Finnish (FIN) AF: 0.915 AC: 9723 AN: 10622

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.974 AC: 66256 AN: 68030

Other (OTH) AF: 0.879 AC: 1854 AN: 2110

Alfa AF: 0.932 Hom.: 251193

Bravo AF: 0.843

Asia WGS AF: 0.675 AC: 2350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.28
DANN	Benign	0.29
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1951033; hg19: chr14-101135318;