rs2899976

Variant names:

• chr14-46354284-G-A
• rs2899976
• ENST00000555246.5:n.299+35423G>A

Variant summary

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

The ENST00000555246.5(LINC00871):​n.299+35423G>A variant causes a intron 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 ENST00000555246.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573
• 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=-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 rank	MANE	Protein	UniProt
LINC00871	NR_102701.1	n.233-83897G>A		intron_variant	Intron 3 of 5
LINC00871	NR_102702.1	n.232+142480G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00871	ENST00000555246.5	n.299+35423G>A		intron_variant	Intron 4 of 5	5
LINC00871	ENST00000556886.1	n.233-83897G>A		intron_variant	Intron 3 of 5	3
LINC00871	ENST00000656720.1	n.233+142480G>A		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.323 AC: 13373 AN: 41384

American (AMR) AF: 0.265 AC: 4031 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1317 AN: 3464

East Asian (EAS) AF: 0.0299 AC: 155 AN: 5178

South Asian (SAS) AF: 0.333 AC: 1606 AN: 4822

European-Finnish (FIN) AF: 0.459 AC: 4800 AN: 10458

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29232 AN: 67654

Other (OTH) AF: 0.364 AC: 764 AN: 2098

Alfa AF: 0.379 Hom.: 1734

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
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs2899976; hg19: chr14-46823487;