rs16968869

Variant names:

• chr19-27923178-G-A
• rs16968869
• ENST00000586408.1:n.235-2839G>A

Variant summary

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

The ENST00000586408.1(ENSG00000267630):​n.235-2839G>A variant causes a intron 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: ENSG00000267630 ENST00000586408.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 0 publications found

Genes affected

ENSG00000267630 (HGNC:):

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

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000586408.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02987	NR_146733.1		n.258+3320G>A		intron	N/A
	LINC02987	NR_146734.1		n.299+3320G>A		intron	N/A
	LINC02987	NR_146735.1		n.1058+3320G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267630	ENST00000586408.1	TSL:6	n.235-2839G>A		intron	N/A
	LINC02987	ENST00000586473.3	TSL:2	n.100+20484G>A		intron	N/A
	LINC02987	ENST00000588122.6	TSL:5	n.857+3320G>A		intron	N/A

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

African (AFR) AF: 0.0870 AC: 3608 AN: 41458

American (AMR) AF: 0.0638 AC: 974 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0895 AC: 310 AN: 3464

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5168

South Asian (SAS) AF: 0.115 AC: 552 AN: 4816

European-Finnish (FIN) AF: 0.0509 AC: 536 AN: 10538

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.0609 AC: 4141 AN: 68002

Other (OTH) AF: 0.0830 AC: 175 AN: 2108

Alfa AF: 0.0703 Hom.: 155

Bravo AF: 0.0678

Asia WGS AF: 0.0690 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.9
DANN	Benign	0.79
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs16968869; hg19: chr19-28414086;