Variant chr10-62622902-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000395251.5(LINC02929):n.151-20840G>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 0.142 in 150,264 control chromosomes in the GnomAD database, including 1,741 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.14 ( 1741 hom., cov: 31)

Consequence

LINC02929
ENST00000395251.5 intron, non_coding_transcript

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.04

Variant links:

Genes affected

LINC02929 (HGNC:55812): (long intergenic non-protein coding RNA 2929)

LINC02929 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 10-62622902-G-A is Benign according to our data. Variant chr10-62622902-G-A is described in ClinVar as [Benign]. Clinvar id is 1266745.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02929	ENST00000395251.5 linkuse as main transcript	n.151-20840G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.142

AC:

21347

AN:

150142

Hom.:

1740

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.220

Gnomad AMR

AF:

0.0897

Gnomad ASJ

AF:

0.159

Gnomad EAS

AF:

0.0146

Gnomad SAS

AF:

0.0570

Gnomad FIN

AF:

0.198

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.176

Gnomad OTH

AF:

0.122

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

GnomAD4 genome

AF:

0.142

AC:

21368

AN:

150264

Hom.:

1741

Cov.:

AF XY:

0.140

AC XY:

10236

AN XY:

73310

show subpopulations

Gnomad4 AFR

AF:

0.115

Gnomad4 AMR

AF:

0.0896

Gnomad4 ASJ

AF:

0.159

Gnomad4 EAS

AF:

0.0147

Gnomad4 SAS

AF:

0.0574

Gnomad4 FIN

AF:

0.198

Gnomad4 NFE

AF:

0.176

Gnomad4 OTH

AF:

0.123

Alfa

AF:

0.167

Hom.:

281

Bravo

AF:

0.132

Asia WGS

AF:

0.0620

AC:

218

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 17, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.83

DANN

Benign

0.26

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over