rs4692824

chr4-170367322-A-G

Variant summary

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

The ENST00000509548.2(LINC02512):n.128-4688A>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 0.635 in 151,942 control chromosomes in the GnomAD database, including 31,776 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 0.63 (31776 hom., cov: 31)
• Consequence: LINC02512 ENST00000509548.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238

Genes affected

LINC02512 (HGNC:53501): (long intergenic non-protein coding RNA 2512)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02512	XR_001741530.1	n.395+16667A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02512	ENST00000509548.2	n.128-4688A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96369 AN: 151824 Hom.: 31760 Cov.: 31

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.0924

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.635 AC: 96430 AN: 151942 Hom.: 31776 Cov.: 31 AF XY: 0.627 AC XY: 46552 AN XY: 74260

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.0928

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.642

Alfa AF: 0.687 Hom.: 74170

Bravo AF: 0.639

Asia WGS AF: 0.286 AC: 997 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.1
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4692824; hg19: chr4-171288473;