rs10143250

Variant names:

• chr14-104257096-C-T
• rs10143250
• ENST00000553757.1:n.234-30390C>T

Variant summary

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

The ENST00000553757.1(LINC02691):​n.234-30390C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 152,064 control chromosomes in the GnomAD database, including 18,991 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 0.48 (18991 hom., cov: 32)
• Consequence: LINC02691 ENST00000553757.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323
• Publications: 14 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02691	NR_146612.1	n.234-30390C>T		intron_variant	Intron 1 of 2
LINC02691	NR_146613.1	n.234-18248C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02691	ENST00000553757.1	n.234-30390C>T		intron_variant	Intron 1 of 2	4
LINC02691	ENST00000556528.1	n.224-18248C>T		intron_variant	Intron 1 of 1	4
LINC02691	ENST00000740132.1	n.233+33280C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73301 AN: 151946 Hom.: 18990 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.482 AC: 73329 AN: 152064 Hom.: 18991 Cov.: 32 AF XY: 0.482 AC XY: 35834 AN XY: 74332

African (AFR) AF: 0.288 AC: 11932 AN: 41502

American (AMR) AF: 0.478 AC: 7302 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1774 AN: 3468

East Asian (EAS) AF: 0.439 AC: 2269 AN: 5174

South Asian (SAS) AF: 0.547 AC: 2632 AN: 4812

European-Finnish (FIN) AF: 0.535 AC: 5653 AN: 10560

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39988 AN: 67952

Other (OTH) AF: 0.524 AC: 1104 AN: 2108

Alfa AF: 0.554 Hom.: 31416

Bravo AF: 0.467

Asia WGS AF: 0.498 AC: 1731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.40
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs10143250; hg19: chr14-104723433;