rs16968869

Positions:

• chr19-27923178-G-A

Variant summary

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

The NR_146733.1(LINC02987):​n.258+3320G>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 0.0682 in 152,026 control chromosomes in the GnomAD database, including 426 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 0.068 (426 hom., cov: 32)
• Consequence: LINC02987 NR_146733.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23

Genes affected

(HGNC:):

LINC02987 (HGNC:56093): (long intergenic non-protein coding RNA 2987)

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 (SAS) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02987	NR_146733.1	n.258+3320G>A		intron_variant, non_coding_transcript_variant
LINC02987	NR_146734.1	n.299+3320G>A		intron_variant, non_coding_transcript_variant
LINC02987	NR_146735.1	n.1058+3320G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000586408.1	n.235-2839G>A		intron_variant, non_coding_transcript_variant
	ENST00000586473.2	n.100+20484G>A		intron_variant, non_coding_transcript_variant		2
LINC02987	ENST00000592806.1	n.242+3320G>A		intron_variant, non_coding_transcript_variant		3
LINC02987	ENST00000667566.1	n.269+3320G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0682 AC: 10364 AN: 151908 Hom.: 427 Cov.: 32

Gnomad AFR AF: 0.0872

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.0639

Gnomad ASJ AF: 0.0895

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0509

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.0609

Gnomad OTH AF: 0.0839

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

GnomAD4 genome AF: 0.0682 AC: 10367 AN: 152026 Hom.: 426 Cov.: 32 AF XY: 0.0694 AC XY: 5158 AN XY: 74306

Gnomad4 AFR AF: 0.0870

Gnomad4 AMR AF: 0.0638

Gnomad4 ASJ AF: 0.0895

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0509

Gnomad4 NFE AF: 0.0609

Gnomad4 OTH AF: 0.0830

Alfa AF: 0.0652 Hom.: 52

Bravo AF: 0.0678

Asia WGS AF: 0.0690 AC: 239 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	7.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16968869; hg19: chr19-28414086;