Variant 10-62655653-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The XM_047426120.1(LOC124902436):c.241+172T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 1,611,916 control chromosomes in the GnomAD database, including 108,528 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 7985 hom., cov: 32)

Exomes 𝑓: 0.36 ( 100543 hom. )

Consequence

LOC124902436
XM_047426120.1 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.124

Variant links:

Genes affected

LOC124902436 (HGNC:):

LOC124902436 links:

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 -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.29).

BP6

Variant 10-62655653-T-A is Benign according to our data. Variant chr10-62655653-T-A is described in ClinVar as [Benign]. Clinvar id is 1273577.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein
LOC124902436	XM_047426120.1 linkuse as main transcript	c.241+172T>A	intron_variant	XP_047282076.1
LOC124902436	XM_047426118.1 linkuse as main transcript	c.397+172T>A	intron_variant	XP_047282074.1
LOC124902436	XM_047426119.1 linkuse as main transcript	c.397+172T>A	intron_variant	XP_047282075.1
LOC124902436	XM_047426121.1 linkuse as main transcript	c.547+22T>A	intron_variant	XP_047282077.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02929	ENST00000395251.5 linkuse as main transcript	n.725+22T>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.296

AC:

45030

AN:

151954

Hom.:

7989

Cov.:

show subpopulations

Gnomad AFR

AF:

0.118

Gnomad AMI

AF:

0.452

Gnomad AMR

AF:

0.221

Gnomad ASJ

AF:

0.396

Gnomad EAS

AF:

0.587

Gnomad SAS

AF:

0.383

Gnomad FIN

AF:

0.367

Gnomad MID

AF:

0.332

Gnomad NFE

AF:

0.375

Gnomad OTH

AF:

0.299

GnomAD3 exomes

AF:

0.347

AC:

86062

AN:

248354

Hom.:

16774

AF XY:

0.358

AC XY:

48081

AN XY:

134414

show subpopulations

Gnomad AFR exome

AF:

0.115

Gnomad AMR exome

AF:

0.159

Gnomad ASJ exome

AF:

0.417

Gnomad EAS exome

AF:

0.609

Gnomad SAS exome

AF:

0.383

Gnomad FIN exome

AF:

0.379

Gnomad NFE exome

AF:

0.372

Gnomad OTH exome

AF:

0.344

GnomAD4 exome

AF:

0.364

AC:

531916

AN:

1459844

Hom.:

100543

Cov.:

AF XY:

0.366

AC XY:

265919

AN XY:

726026

show subpopulations

Gnomad4 AFR exome

AF:

0.109

Gnomad4 AMR exome

AF:

0.167

Gnomad4 ASJ exome

AF:

0.407

Gnomad4 EAS exome

AF:

0.544

Gnomad4 SAS exome

AF:

0.387

Gnomad4 FIN exome

AF:

0.368

Gnomad4 NFE exome

AF:

0.372

Gnomad4 OTH exome

AF:

0.350

GnomAD4 genome

AF:

0.296

AC:

45014

AN:

152072

Hom.:

7985

Cov.:

AF XY:

0.297

AC XY:

22086

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.118

Gnomad4 AMR

AF:

0.220

Gnomad4 ASJ

AF:

0.396

Gnomad4 EAS

AF:

0.587

Gnomad4 SAS

AF:

0.382

Gnomad4 FIN

AF:

0.367

Gnomad4 NFE

AF:

0.375

Gnomad4 OTH

AF:

0.295

Alfa

AF:

0.339

Hom.:

1702

Bravo

AF:

0.276

Asia WGS

AF:

0.409

AC:

1422

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 16, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.29

CADD

Benign

DANN

Benign

0.82

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