Variant chr10-62670237-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The XM_047426120.1(LOC124902436):c.437A>G(p.Glu146Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000781 in 1,613,634 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0040 ( 7 hom., cov: 32)

Exomes 𝑓: 0.00044 ( 11 hom. )

Consequence

LOC124902436
XM_047426120.1 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0100

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 -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004766792).

BP6

Variant 10-62670237-A-G is Benign according to our data. Variant chr10-62670237-A-G is described in ClinVar as [Benign]. Clinvar id is 786160.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein
LOC124902436	XM_047426120.1 linkuse as main transcript	c.437A>G	p.Glu146Gly	missense_variant	6/6	XP_047282076.1
LOC124902436	XM_047426121.1 linkuse as main transcript	c.743A>G	p.Glu248Gly	missense_variant	6/6	XP_047282077.1
LOC124902436	XM_047426118.1 linkuse as main transcript	c.593A>G	p.Glu198Gly	missense_variant	6/6	XP_047282074.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
LINC02929	ENST00000344640.7 linkuse as main transcript	n.401A>G	non_coding_transcript_exon_variant	4/4	1
LINC02929	ENST00000373784.6 linkuse as main transcript	n.475A>G	non_coding_transcript_exon_variant	5/5	1
LINC02929	ENST00000395249.5 linkuse as main transcript	n.296A>G	non_coding_transcript_exon_variant	3/3	1
LINC02929	ENST00000395251.5 linkuse as main transcript	n.921A>G	non_coding_transcript_exon_variant	7/7	1

Frequencies

GnomAD3 genomes

AF:

0.00400

AC:

609

AN:

152120

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0139

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000982

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0000882

Gnomad OTH

AF:

0.00526

GnomAD3 exomes

AF:

0.000939

AC:

236

AN:

251296

Hom.:

AF XY:

0.000751

AC XY:

102

AN XY:

135816

show subpopulations

Gnomad AFR exome

AF:

0.0118

Gnomad AMR exome

AF:

0.000781

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000131

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000616

Gnomad OTH exome

AF:

0.00114

GnomAD4 exome

AF:

0.000443

AC:

648

AN:

1461396

Hom.:

Cov.:

AF XY:

0.000387

AC XY:

281

AN XY:

727018

show subpopulations

Gnomad4 AFR exome

AF:

0.0135

Gnomad4 AMR exome

AF:

0.000962

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000580

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000675

Gnomad4 OTH exome

AF:

0.00108

GnomAD4 genome

AF:

0.00403

AC:

613

AN:

152238

Hom.:

Cov.:

AF XY:

0.00381

AC XY:

284

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.0140

Gnomad4 AMR

AF:

0.000981

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000882

Gnomad4 OTH

AF:

0.00520

Alfa

AF:

0.000652

Hom.:

Bravo

AF:

0.00450

TwinsUK

AF:

0.00

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.0127

AC:

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.00117

AC:

142

Asia WGS

AF:

0.00260

AC:

AN:

3478

EpiCase

AF:

0.000109

EpiControl

AF:

0.000119

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 11, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.60

CADD

Benign

1.8

DANN

Benign

0.50

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.028

LIST_S2

Benign

0.42

T;T

MetaRNN

Benign

0.0048

T;T

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

N;N;N

PrimateAI

Benign

0.29

PROVEAN

Benign

-0.48

N;.

REVEL

Benign

0.060

Sift

Pathogenic

0.0

D;.

Sift4G

Pathogenic

0.0

D;D

Polyphen

0.0010

B;.

Vest4

0.10

MVP

0.11

MPC

0.25

ClinPred

0.013

GERP RS

-1.3

gMVP

0.060

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