rs2887987

chr2-34364072-C-Achr2-34364072-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01320	ENST00000650021.1	n.167-20445C>A		intron_variant, non_coding_transcript_variant

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;