chr3-10284485-G-A

Position:

• chr3-10284485-G-A

Variant summary

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

The NR_026829.1(LINC00852):​n.67G>A 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 0.64 in 152,074 control chromosomes in the GnomAD database, including 32,399 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 0.64 (32385 hom., cov: 31)
  • Exomes 𝑓: 0.61 (14 hom.)
• Consequence: LINC00852 NR_026829.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00852	NR_026829.1	n.67G>A		non_coding_transcript_exon_variant	1/1
GHRLOS	NR_024145.2	n.291+882G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00852	ENST00000475197.1	n.67G>A		non_coding_transcript_exon_variant	1/1
LINC00852	ENST00000538717.1	n.67G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97201 AN: 151892 Hom.: 32346 Cov.: 31

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.617

GnomAD4 exome AF: 0.609 AC: 39 AN: 64 Hom.: 14 Cov.: 0 AF XY: 0.640 AC XY: 32 AN XY: 50

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.605

Gnomad4 OTH exome AF: 0.700

GnomAD4 genome AF: 0.640 AC: 97299 AN: 152010 Hom.: 32385 Cov.: 31 AF XY: 0.649 AC XY: 48184 AN XY: 74268

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.955

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.615

Alfa AF: 0.549 Hom.: 38368

Bravo AF: 0.656

Asia WGS AF: 0.845 AC: 2936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.76
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs171407; hg19: chr3-10326169;