rs10143250

Positions:

• chr14-104257096-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_146612.1(LINC02691):​n.234-30390C>T 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 0.482 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 NR_146612.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02691	NR_146612.1	n.234-30390C>T		intron_variant, non_coding_transcript_variant
LINC02691	NR_146613.1	n.234-18248C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02691	ENST00000553757.1	n.234-30390C>T		intron_variant, non_coding_transcript_variant		4
LINC02691	ENST00000556528.1	n.224-18248C>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.524

Alfa AF: 0.567 Hom.: 25215

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10143250; hg19: chr14-104723433;