dbSNP rs10125054: LINC02977:n.1286C>T (chr9-112035757-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000563434.1(LINC02977):n.1286C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,142 control chromosomes in the GnomAD database, including 5,575 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 0.27 ( 5575 hom., cov: 32)

Exomes 𝑓: 0.33 ( 0 hom. )

Consequence

LINC02977
ENST00000563434.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.793

Variant links:

Genes affected

LINC02977 (HGNC:56036): (long intergenic non-protein coding RNA 2977)

LINC02977 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02977	NR_186812.1 link	n.2246+2422C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02977	ENST00000563434.1 link	n.1286C>T	non_coding_transcript_exon_variant	Exon 2 of 2	2
LINC02977	ENST00000568421.1 link	n.554C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC02977	ENST00000658557.1 link	n.965+2422C>T	intron_variant	Intron 1 of 2
LINC02977	ENST00000563249.1 link	n.*104C>T	downstream_gene_variant		4

Frequencies

GnomAD3 genomes

AF:

0.268

AC:

40789

AN:

152020

Hom.:

5579

Cov.:

show subpopulations

Gnomad AFR

AF:

0.285

Gnomad AMI

AF:

0.182

Gnomad AMR

AF:

0.263

Gnomad ASJ

AF:

0.294

Gnomad EAS

AF:

0.397

Gnomad SAS

AF:

0.314

Gnomad FIN

AF:

0.310

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.239

Gnomad OTH

AF:

0.278

GnomAD4 exome

AF:

0.333

AC:

AN:

Hom.:

Cov.:

AF XY:

0.333

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.250

GnomAD4 genome

AF:

0.268

AC:

40806

AN:

152136

Hom.:

5575

Cov.:

AF XY:

0.273

AC XY:

20338

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.285

Gnomad4 AMR

AF:

0.263

Gnomad4 ASJ

AF:

0.294

Gnomad4 EAS

AF:

0.396

Gnomad4 SAS

AF:

0.314

Gnomad4 FIN

AF:

0.310

Gnomad4 NFE

AF:

0.239

Gnomad4 OTH

AF:

0.276

Alfa

AF:

0.248

Hom.:

4968

Bravo

AF:

0.266

Asia WGS

AF:

0.330

AC:

1145

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

7.2

DANN

Benign

0.73

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over