Variant chr10-62656460-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The XM_047426120.1(LOC124902436):c.306C>T(p.Asp102=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00287 in 780,904 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0022 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0030 ( 27 hom. )

Consequence

LOC124902436
XM_047426120.1 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.518

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 10-62656460-C-T is Benign according to our data. Variant chr10-62656460-C-T is described in ClinVar as [Benign]. Clinvar id is 773798.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.518 with no splicing effect.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00215 (328/152270) while in subpopulation EAS AF= 0.0474 (245/5174). AF 95% confidence interval is 0.0425. There are 5 homozygotes in gnomad4. There are 158 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein
LOC124902436	XM_047426120.1 linkuse as main transcript	c.306C>T	p.Asp102=	synonymous_variant	4/6	XP_047282076.1
LOC124902436	XM_047426121.1 linkuse as main transcript	c.612C>T	p.Asp204=	synonymous_variant	4/6	XP_047282077.1
LOC124902436	XM_047426118.1 linkuse as main transcript	c.462C>T	p.Asp154=	synonymous_variant	4/6	XP_047282074.1
LOC124902436	XM_047426119.1 linkuse as main transcript	c.462C>T	p.Asp154=	synonymous_variant	4/5	XP_047282075.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02929	ENST00000395251.5 linkuse as main transcript	n.790C>T		non_coding_transcript_exon_variant	5/7	1

Frequencies

GnomAD3 genomes

AF:

0.00217

AC:

330

AN:

152150

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000193

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00367

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0476

Gnomad SAS

AF:

0.00249

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000441

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00614

AC:

1529

AN:

249038

Hom.:

AF XY:

0.00514

AC XY:

693

AN XY:

134814

show subpopulations

Gnomad AFR exome

AF:

0.000123

Gnomad AMR exome

AF:

0.0155

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0502

Gnomad SAS exome

AF:

0.00150

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000449

Gnomad OTH exome

AF:

0.00245

GnomAD4 exome

AF:

0.00304

AC:

1912

AN:

628634

Hom.:

Cov.:

AF XY:

0.00267

AC XY:

916

AN XY:

342466

show subpopulations

Gnomad4 AFR exome

AF:

0.000170

Gnomad4 AMR exome

AF:

0.0147

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0295

Gnomad4 SAS exome

AF:

0.00196

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000657

Gnomad4 OTH exome

AF:

0.00127

GnomAD4 genome

AF:

0.00215

AC:

328

AN:

152270

Hom.:

Cov.:

AF XY:

0.00212

AC XY:

158

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.000192

Gnomad4 AMR

AF:

0.00366

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0474

Gnomad4 SAS

AF:

0.00249

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000441

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00216

Hom.:

Bravo

AF:

0.00352

Asia WGS

AF:

0.0210

AC:

AN:

3478

EpiCase

AF:

0.000109

EpiControl

AF:

0.00

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 19, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	May 11, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

7.3

DANN

Benign

0.39

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