Variant rs7068008 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000659883.1(LINC02930):n.195-144A>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 0.582 in 152,050 control chromosomes in the GnomAD database, including 26,101 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 0.58 ( 26101 hom., cov: 32)

Consequence

LINC02930
ENST00000659883.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.381

Variant links:

Genes affected

LINC02930 (HGNC:55821): (long intergenic non-protein coding RNA 2930)

LINC02930 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=-0.88).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02930	XR_002957103.2 linkuse as main transcript	n.193-144A>G		intron_variant, non_coding_transcript_variant
LINC02930	XR_007062314.1 linkuse as main transcript	n.852A>G		non_coding_transcript_exon_variant	1/5

Ensembl

Gene	Transcript	HGVSc	Effect
LINC02930	ENST00000659883.1 linkuse as main transcript	n.195-144A>G	intron_variant, non_coding_transcript_variant
LINC02930	ENST00000655330.1 linkuse as main transcript	n.133-144A>G	intron_variant, non_coding_transcript_variant
LINC02930	ENST00000663713.1 linkuse as main transcript	n.193-144A>G	intron_variant, non_coding_transcript_variant
LINC02930	ENST00000665554.1 linkuse as main transcript	n.178-144A>G	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.582

AC:

88423

AN:

151932

Hom.:

26081

Cov.:

show subpopulations

Gnomad AFR

AF:

0.619

Gnomad AMI

AF:

0.618

Gnomad AMR

AF:

0.666

Gnomad ASJ

AF:

0.614

Gnomad EAS

AF:

0.601

Gnomad SAS

AF:

0.553

Gnomad FIN

AF:

0.545

Gnomad MID

AF:

0.718

Gnomad NFE

AF:

0.544

Gnomad OTH

AF:

0.605

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

GnomAD4 genome

AF:

0.582

AC:

88479

AN:

152050

Hom.:

26101

Cov.:

AF XY:

0.584

AC XY:

43383

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.619

Gnomad4 AMR

AF:

0.666

Gnomad4 ASJ

AF:

0.614

Gnomad4 EAS

AF:

0.602

Gnomad4 SAS

AF:

0.550

Gnomad4 FIN

AF:

0.545

Gnomad4 NFE

AF:

0.544

Gnomad4 OTH

AF:

0.599

Alfa

AF:

0.562

Hom.:

35395

Bravo

AF:

0.594

Asia WGS

AF:

0.552

AC:

1922

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.6

DANN

Benign

0.78

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