rs886716

Positions:

• chr7-26517999-A-G

Variant summary

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

The NR_148499.1(LINC02981):​n.1386-20254A>G 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 0.371 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: LINC02981 NR_148499.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535

Genes affected

LINC02981 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02981	NR_148499.1	n.1386-20254A>G		intron_variant, non_coding_transcript_variant
LINC02981	NR_148500.1	n.981-20254A>G		intron_variant, non_coding_transcript_variant
LINC02981	NR_148501.1	n.1264-20254A>G		intron_variant, non_coding_transcript_variant
LINC02981	NR_148502.1	n.1209-20254A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.0661

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.308

Alfa AF: 0.306 Hom.: 16590

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs886716; hg19: chr7-26557618;