12-74258017-T-G

Position:

• chr12-74258017-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.473+27008A>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 0.091 in 152,142 control chromosomes in the GnomAD database, including 737 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 0.091 (737 hom., cov: 32)
• Consequence: LINC02882 NR_038300.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02882	NR_038300.1	n.473+27008A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000552046.1	n.222-7436A>C		intron_variant, non_coding_transcript_variant		3
LINC02882	ENST00000663261.1	n.565+27008A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0911 AC: 13844 AN: 152024 Hom.: 740 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0614

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.0733

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.0734

Gnomad OTH AF: 0.0831

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

GnomAD4 genome AF: 0.0910 AC: 13846 AN: 152142 Hom.: 737 Cov.: 32 AF XY: 0.0899 AC XY: 6683 AN XY: 74366

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.0613

Gnomad4 ASJ AF: 0.0945

Gnomad4 EAS AF: 0.0129

Gnomad4 SAS AF: 0.0721

Gnomad4 FIN AF: 0.0532

Gnomad4 NFE AF: 0.0734

Gnomad4 OTH AF: 0.0822

Alfa AF: 0.0700 Hom.: 244

Bravo AF: 0.0941

Asia WGS AF: 0.0430 AC: 150 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7294453; hg19: chr12-74651797;