3-10285002-A-G

Position:

• chr3-10285002-A-G

Variant summary

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

The NR_026829.1(LINC00852):​n.584A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 153,804 control chromosomes in the GnomAD database, including 6,637 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 0.28 (6610 hom., cov: 33)
  • Exomes 𝑓: 0.22 (27 hom.)
• Consequence: LINC00852 NR_026829.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48

Genes affected

LINC00852 (HGNC:29904): (long intergenic non-protein coding RNA 852)

GHRLOS (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00852	NR_026829.1	n.584A>G		non_coding_transcript_exon_variant	1/1
GHRLOS	NR_024145.2	n.292-746A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00852	ENST00000475197.1	n.584A>G		non_coding_transcript_exon_variant	1/1
LINC00852	ENST00000538717.1	n.584A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43286 AN: 152088 Hom.: 6597 Cov.: 33

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.0260

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.288

GnomAD4 exome AF: 0.217 AC: 346 AN: 1598 Hom.: 27 Cov.: 0 AF XY: 0.203 AC XY: 170 AN XY: 838

Gnomad4 FIN exome AF: 0.213

Gnomad4 NFE exome AF: 0.344

Gnomad4 OTH exome AF: 0.300

GnomAD4 genome AF: 0.285 AC: 43342 AN: 152206 Hom.: 6610 Cov.: 33 AF XY: 0.279 AC XY: 20758 AN XY: 74442

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.0258

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.284

Alfa AF: 0.258 Hom.: 2888

Bravo AF: 0.287

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.015
DANN	Benign	0.26

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs35684; hg19: chr3-10326686; COSMIC: COSV55051957;