Variant 10-62666153-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The XM_047426120.1(LOC124902436):c.357C>A(p.Ser119Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000318 in 1,613,104 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0017 ( 2 hom., cov: 32)

Exomes 𝑓: 0.00018 ( 3 hom. )

Consequence

LOC124902436
XM_047426120.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.163

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0049355626).

BP6

Variant 10-62666153-C-A is Benign according to our data. Variant chr10-62666153-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 786159.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein
LOC124902436	XM_047426120.1 linkuse as main transcript	c.357C>A	p.Ser119Arg	missense_variant	5/6	XP_047282076.1
LOC124902436	XM_047426121.1 linkuse as main transcript	c.663C>A	p.Ser221Arg	missense_variant	5/6	XP_047282077.1
LOC124902436	XM_047426118.1 linkuse as main transcript	c.513C>A	p.Ser171Arg	missense_variant	5/6	XP_047282074.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
LINC02929	ENST00000373784.6 linkuse as main transcript	n.395C>A	non_coding_transcript_exon_variant	4/5	1
LINC02929	ENST00000395249.5 linkuse as main transcript	n.216C>A	non_coding_transcript_exon_variant	2/3	1
LINC02929	ENST00000395251.5 linkuse as main transcript	n.841C>A	non_coding_transcript_exon_variant	6/7	1
LINC02929	ENST00000344640.7 linkuse as main transcript	n.371-4054C>A	intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.00168

AC:

256

AN:

152026

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00598

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000393

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000147

Gnomad OTH

AF:

0.000957

GnomAD3 exomes

AF:

0.000386

AC:

AN:

251256

Hom.:

AF XY:

0.000280

AC XY:

AN XY:

135790

show subpopulations

Gnomad AFR exome

AF:

0.00548

Gnomad AMR exome

AF:

0.000174

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000880

Gnomad OTH exome

AF:

0.000163

GnomAD4 exome

AF:

0.000175

AC:

256

AN:

1460960

Hom.:

Cov.:

AF XY:

0.000138

AC XY:

100

AN XY:

726844

show subpopulations

Gnomad4 AFR exome

AF:

0.00614

Gnomad4 AMR exome

AF:

0.000157

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000116

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

9.00e-7

Gnomad4 OTH exome

AF:

0.000663

GnomAD4 genome

AF:

0.00169

AC:

257

AN:

152144

Hom.:

Cov.:

AF XY:

0.00160

AC XY:

119

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.00598

Gnomad4 AMR

AF:

0.000392

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000147

Gnomad4 OTH

AF:

0.000947

Alfa

AF:

0.000329

Hom.:

Bravo

AF:

0.00186

ESP6500AA

AF:

0.00499

AC:

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.000445

AC:

Asia WGS

AF:

0.00173

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely 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

-0.49

BayesDel_noAF

Benign

-0.47

CADD

Benign

0.96

DANN

Benign

0.95

Eigen

Benign

-0.93

Eigen_PC

Benign

-0.98

FATHMM_MKL

Benign

0.087

LIST_S2

Benign

0.46

T;T

M_CAP

Benign

0.014

MetaRNN

Benign

0.0049

T;T

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

N;N;N

PrimateAI

Benign

0.34

PROVEAN

Benign

-0.55

N;.

REVEL

Benign

0.057

Sift

Uncertain

0.014

D;.

Sift4G

Uncertain

0.042

D;T

Polyphen

0.0090

B;.

Vest4

0.43

MutPred

0.14

.;Gain of catalytic residue at S169 (P = 0.0608);

MVP

0.15

MPC

0.51

ClinPred

0.053

GERP RS

0.060

gMVP

0.038

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