rs1373877

chr12-64982742-T-C

Variant summary

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

The NR_146276.1(LINC02231):n.16-220A>G 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 0.433 in 152,008 control chromosomes in the GnomAD database, including 14,719 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 0.43 (14719 hom., cov: 32)
• Consequence: LINC02231 NR_146276.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

LINC02389 (HGNC:53316): (long intergenic non-protein coding RNA 2389)

LINC02231 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02231	NR_146276.1	n.16-220A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02389	ENST00000662789.1	n.249-316T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65797 AN: 151888 Hom.: 14726 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.433 AC: 65809 AN: 152008 Hom.: 14719 Cov.: 32 AF XY: 0.429 AC XY: 31872 AN XY: 74300

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.470

Alfa AF: 0.473 Hom.: 19514

Bravo AF: 0.432

Asia WGS AF: 0.272 AC: 947 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.4
Dann	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1373877; hg19: chr12-65376522;