rs3987

Positions:

• chr4-117837900-A-G

Variant summary

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

The NR_147154.1(LINC02264):​n.86+3414A>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 0.547 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 NR_147154.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.675

Genes affected

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

LOC102723914 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02264	NR_147154.1	n.86+3414A>G		intron_variant, non_coding_transcript_variant
LOC102723914	XR_427579.4	n.72-9624T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02264	ENST00000669974.1	n.90+3666A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.851

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.550

Alfa AF: 0.480 Hom.: 3291

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3987; hg19: chr4-118759055;