rs10506701

chr12-74192430-T-G

Variant summary

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

The NR_038300.1(LINC02882):n.553+1644A>C 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 0.153 in 152,188 control chromosomes in the GnomAD database, including 2,192 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 0.15 (2192 hom., cov: 32)
• Consequence: LINC02882 NR_038300.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144

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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02882	NR_038300.1	n.553+1644A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02882	ENST00000663261.1	n.566-34546A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23330 AN: 152070 Hom.: 2192 Cov.: 32

Gnomad AFR AF: 0.0617

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.0528

Gnomad SAS AF: 0.0999

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.153 AC: 23335 AN: 152188 Hom.: 2192 Cov.: 32 AF XY: 0.152 AC XY: 11318 AN XY: 74376

Gnomad4 AFR AF: 0.0616

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.0529

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.147

Alfa AF: 0.188 Hom.: 4176

Bravo AF: 0.149

Asia WGS AF: 0.101 AC: 352 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	1.7
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506701; hg19: chr12-74586210;