rs4530059

Variant names:

• chr14-104302812-G-A
• rs4530059
• ENST00000740132.1:n.234-12604G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-104302812-G-A
• chr14-104302812-G-T

Variant summary

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

The ENST00000740132.1(LINC02691):​n.234-12604G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,178 control chromosomes in the GnomAD database, including 9,284 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 0.35 (9284 hom., cov: 34)
• Consequence: LINC02691 ENST00000740132.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771
• Publications: 17 publications found

Genes affected

LINC02691 (HGNC:20358): (long intergenic non-protein coding RNA 2691)

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 (AMR) allele frequency at 95% confidence interval = 0.397 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
LINC02691	ENST00000740132.1	n.234-12604G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52776 AN: 152060 Hom.: 9285 Cov.: 34

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.347 AC: 52792 AN: 152178 Hom.: 9284 Cov.: 34 AF XY: 0.349 AC XY: 25934 AN XY: 74394

African (AFR) AF: 0.326 AC: 13528 AN: 41506

American (AMR) AF: 0.405 AC: 6195 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1556 AN: 3472

East Asian (EAS) AF: 0.279 AC: 1449 AN: 5186

South Asian (SAS) AF: 0.231 AC: 1112 AN: 4824

European-Finnish (FIN) AF: 0.406 AC: 4300 AN: 10590

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23599 AN: 67988

Other (OTH) AF: 0.355 AC: 750 AN: 2114

Alfa AF: 0.330 Hom.: 6935

Bravo AF: 0.351

Asia WGS AF: 0.272 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.80
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs4530059; hg19: chr14-104769149;