rs12989577

Variant names:

• chr2-107581433-G-A
• rs12989577
• ENST00000654481.1:n.326-52569C>T

Variant summary

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

The ENST00000654481.1(LINC01885):​n.326-52569C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,994 control chromosomes in the GnomAD database, including 20,915 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 0.48 (20915 hom., cov: 32)
• Consequence: LINC01885 ENST00000654481.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

Genes affected

LINC01885 (HGNC:52704): (long intergenic non-protein coding RNA 1885)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01885	ENST00000654481.1	n.326-52569C>T		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73035 AN: 151874 Hom.: 20906 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.481 AC: 73060 AN: 151994 Hom.: 20915 Cov.: 32 AF XY: 0.476 AC XY: 35371 AN XY: 74290

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.536

Alfa AF: 0.547 Hom.: 4181

Bravo AF: 0.464

Asia WGS AF: 0.501 AC: 1740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0060
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12989577; hg19: chr2-108197889;