rs10498398

chr14-46398286-C-T

Variant summary

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

The NR_102701.1(LINC00871):n.233-39895C>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 0.367 in 151,850 control chromosomes in the GnomAD database, including 10,851 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 0.37 (10851 hom., cov: 32)
• Consequence: LINC00871 NR_102701.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.859

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=-0.58).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00871	NR_102701.1	n.233-39895C>T		intron_variant, non_coding_transcript_variant
LINC00871	NR_102702.1	n.233-103021C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00871	ENST00000666179.1	n.351-103021C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55687 AN: 151732 Hom.: 10851 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.0308

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.367 AC: 55703 AN: 151850 Hom.: 10851 Cov.: 32 AF XY: 0.362 AC XY: 26897 AN XY: 74232

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.0306

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.360

Alfa AF: 0.375 Hom.: 1875

Bravo AF: 0.349

Asia WGS AF: 0.166 AC: 580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
Cadd	Benign	5.2
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498398; hg19: chr14-46867489;