rs2887987

Variant names:

• chr2-34364072-C-A
• rs2887987
• ENST00000650021.1:n.167-20445C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-34364072-C-A
• chr2-34364072-C-G

Variant summary

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

The ENST00000650021.1(LINC01320):​n.167-20445C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 151,966 control chromosomes in the GnomAD database, including 33,435 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 0.66 (33435 hom., cov: 33)
• Consequence: LINC01320 ENST00000650021.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

Genes affected

LINC01320 (HGNC:50526): (long intergenic non-protein coding RNA 1320)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 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
LINC01320	ENST00000650021.1	n.167-20445C>A		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99786 AN: 151848 Hom.: 33420 Cov.: 33

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.657 AC: 99847 AN: 151966 Hom.: 33435 Cov.: 33 AF XY: 0.666 AC XY: 49427 AN XY: 74252

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.944

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.612

Alfa AF: 0.605 Hom.: 2048

Bravo AF: 0.650

Asia WGS AF: 0.772 AC: 2683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.58
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2887987; hg19: chr2-34589139;