14-46463088-G-T

Variant names:

• chr14-46463088-G-T
• rs11846013
• ENST00000556886.1:n.349+13134G>T

Variant summary

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

The ENST00000556886.1(LINC00871):​n.349+13134G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,574 control chromosomes in the GnomAD database, including 8,737 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 0.31 (8737 hom., cov: 32)
• Consequence: LINC00871 ENST00000556886.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

Genes affected

LINC00871 (HGNC:47038): (long intergenic non-protein coding RNA 871)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00871	NR_102701.1	n.349+13134G>T		intron_variant	Intron 5 of 5
LINC00871	NR_102702.1	n.233-38219G>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00871	ENST00000556886.1	n.349+13134G>T		intron_variant	Intron 5 of 5	3
LINC00871	ENST00000656720.1	n.234-38219G>T		intron_variant	Intron 3 of 3
LINC00871	ENST00000664642.1	n.360-8274G>T		intron_variant	Intron 4 of 5
LINC00871	ENST00000666179.1	n.351-38219G>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46780 AN: 151454 Hom.: 8717 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.0750

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.309 AC: 46815 AN: 151574 Hom.: 8737 Cov.: 32 AF XY: 0.308 AC XY: 22801 AN XY: 74054

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.0748

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.348

Alfa AF: 0.351 Hom.: 4089

Bravo AF: 0.323

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11846013; hg19: chr14-46932291;