rs10506703

chr12-74147931-G-A

Variant summary

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

The NR_038300.1(LINC02882):n.697+3071C>T 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 0.169 in 151,882 control chromosomes in the GnomAD database, including 2,349 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 0.17 (2349 hom., cov: 32)
• Consequence: LINC02882 NR_038300.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

Genes affected

LINC02882 (HGNC:54802): (long intergenic non-protein coding RNA 2882)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02882	NR_038300.1	n.697+3071C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02882	ENST00000663261.1	n.709+3071C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25680 AN: 151764 Hom.: 2350 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0633

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.157

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.169 AC: 25686 AN: 151882 Hom.: 2349 Cov.: 32 AF XY: 0.168 AC XY: 12471 AN XY: 74216

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.0630

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.158

Alfa AF: 0.179 Hom.: 371

Bravo AF: 0.166

Asia WGS AF: 0.107 AC: 372 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.9
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506703; hg19: chr12-74541711;