rs886716

Variant names:

• chr7-26517999-A-G
• rs886716
• ENST00000780535.1:n.282+5770A>G

Variant summary

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

The ENST00000780535.1(ENSG00000301643):​n.282+5770A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,130 control chromosomes in the GnomAD database, including 11,926 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 (11926 hom., cov: 33)
• Consequence: ENSG00000301643 ENST00000780535.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535
• Publications: 12 publications found

Genes affected

ENSG00000301643 (HGNC:):

LINC02981 (HGNC:56055): (long intergenic non-protein coding RNA 2981)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02981	NR_148499.1	n.1386-20254A>G		intron_variant	Intron 6 of 6
LINC02981	NR_148500.1	n.981-20254A>G		intron_variant	Intron 5 of 5
LINC02981	NR_148501.1	n.1264-20254A>G		intron_variant	Intron 5 of 5
LINC02981	NR_148502.1	n.1209-20254A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301643	ENST00000780535.1	n.282+5770A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56439 AN: 152012 Hom.: 11919 Cov.: 33

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.0659

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.371 AC: 56470 AN: 152130 Hom.: 11926 Cov.: 33 AF XY: 0.369 AC XY: 27430 AN XY: 74372

African (AFR) AF: 0.586 AC: 24315 AN: 41484

American (AMR) AF: 0.235 AC: 3597 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1115 AN: 3468

East Asian (EAS) AF: 0.0661 AC: 343 AN: 5192

South Asian (SAS) AF: 0.291 AC: 1401 AN: 4820

European-Finnish (FIN) AF: 0.385 AC: 4072 AN: 10572

Middle Eastern (MID) AF: 0.272 AC: 79 AN: 290

European-Non Finnish (NFE) AF: 0.303 AC: 20572 AN: 67984

Other (OTH) AF: 0.308 AC: 652 AN: 2116

Alfa AF: 0.318 Hom.: 36592

Bravo AF: 0.367

Asia WGS AF: 0.198 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.39
DANN	Benign	0.57
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs886716; hg19: chr7-26557618;