rs2899976

Positions:

• chr14-46354284-G-A

Variant summary

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

The NR_102701.1(LINC00871):​n.233-83897G>A 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 0.369 in 151,468 control chromosomes in the GnomAD database, including 10,913 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 (10913 hom., cov: 31)
• Consequence: LINC00871 NR_102701.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573

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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00871	NR_102701.1	n.233-83897G>A		intron_variant, non_coding_transcript_variant
LINC00871	NR_102702.1	n.232+142480G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00871	ENST00000666179.1	n.350+142480G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55805 AN: 151350 Hom.: 10912 Cov.: 31

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.0301

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.369 AC: 55826 AN: 151468 Hom.: 10913 Cov.: 31 AF XY: 0.364 AC XY: 26945 AN XY: 73970

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.0299

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.364

Alfa AF: 0.380 Hom.: 1694

Bravo AF: 0.350

Asia WGS AF: 0.184 AC: 641 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2899976; hg19: chr14-46823487;