rs3987

Variant names:

• chr4-117837900-A-G
• rs3987
• ENST00000442020.1:n.86+3414A>G

Variant summary

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

The ENST00000442020.1(LINC02264):​n.86+3414A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 151,970 control chromosomes in the GnomAD database, including 25,644 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 0.55 (25644 hom., cov: 32)
• Consequence: LINC02264 ENST00000442020.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.675
• Publications: 16 publications found

Genes affected

LINC02264 (HGNC:53176): (long intergenic non-protein coding RNA 2264)

ENSG00000299982 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02264	NR_147154.1	n.86+3414A>G		intron_variant	Intron 1 of 1
LOC102723914	XR_427579.4	n.72-9624T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02264	ENST00000442020.1	n.86+3414A>G		intron_variant	Intron 1 of 1	3
LINC02264	ENST00000655867.1	n.146+3414A>G		intron_variant	Intron 1 of 1
LINC02264	ENST00000658473.2	n.147+3414A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82947 AN: 151852 Hom.: 25588 Cov.: 32

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.547 AC: 83063 AN: 151970 Hom.: 25644 Cov.: 32 AF XY: 0.548 AC XY: 40671 AN XY: 74252

African (AFR) AF: 0.851 AC: 35308 AN: 41484

American (AMR) AF: 0.497 AC: 7594 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1729 AN: 3466

East Asian (EAS) AF: 0.627 AC: 3231 AN: 5154

South Asian (SAS) AF: 0.425 AC: 2051 AN: 4822

European-Finnish (FIN) AF: 0.448 AC: 4723 AN: 10550

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26579 AN: 67912

Other (OTH) AF: 0.550 AC: 1160 AN: 2110

Alfa AF: 0.491 Hom.: 3573

Bravo AF: 0.570

Asia WGS AF: 0.529 AC: 1833 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.041
DANN	Benign	0.51
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs3987; hg19: chr4-118759055;