rs10498398

Variant names:

• chr14-46398286-C-T
• rs10498398
• ENST00000555246.5:n.300-47899C>T

Variant summary

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

The ENST00000555246.5(LINC00871):​n.300-47899C>T variant causes a intron 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 ENST00000555246.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.859
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC00871	NR_102701.1	n.233-39895C>T		intron_variant	Intron 3 of 5
LINC00871	NR_102702.1	n.233-103021C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00871	ENST00000555246.5	n.300-47899C>T		intron_variant	Intron 4 of 5	5
LINC00871	ENST00000556886.1	n.233-39895C>T		intron_variant	Intron 3 of 5	3
LINC00871	ENST00000656720.1	n.234-103021C>T		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.326 AC: 13513 AN: 41410

American (AMR) AF: 0.268 AC: 4084 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1353 AN: 3464

East Asian (EAS) AF: 0.0306 AC: 158 AN: 5158

South Asian (SAS) AF: 0.301 AC: 1454 AN: 4826

European-Finnish (FIN) AF: 0.454 AC: 4767 AN: 10508

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29073 AN: 67908

Other (OTH) AF: 0.360 AC: 758 AN: 2108

Alfa AF: 0.374 Hom.: 1916

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
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs10498398; hg19: chr14-46867489;