Variant 3-125929513-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000340333.7(ENSG00000291096):n.567A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.358 in 1,596,110 control chromosomes in the GnomAD database, including 104,343 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.33 ( 8870 hom., cov: 32)

Exomes 𝑓: 0.36 ( 95473 hom. )

Consequence

ENSG00000291096
ENST00000340333.7 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.93

Variant links:

Genes affected

ENSG00000291096 (HGNC:):

ENSG00000291096 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.013293445).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
FAM86JP	NR_024250.1 linkuse as main transcript	n.1432T>C	non_coding_transcript_exon_variant	5/5
FAM86JP	NR_024251.1 linkuse as main transcript	n.1530T>C	non_coding_transcript_exon_variant	5/5
ALG1L1P	NR_171194.1 linkuse as main transcript	n.818A>G	non_coding_transcript_exon_variant	7/7

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
ENSG00000291096	ENST00000340333.7 linkuse as main transcript	n.567A>G	non_coding_transcript_exon_variant	6/6	1
FAM86JP	ENST00000467239.5 linkuse as main transcript	n.1413T>C	non_coding_transcript_exon_variant	5/5	1
FAM86JP	ENST00000485843.3 linkuse as main transcript	n.1522T>C	non_coding_transcript_exon_variant	5/5	1

Frequencies

GnomAD3 genomes

AF:

0.335

AC:

50864

AN:

151892

Hom.:

8873

Cov.:

show subpopulations

Gnomad AFR

AF:

0.264

Gnomad AMI

AF:

0.348

Gnomad AMR

AF:

0.274

Gnomad ASJ

AF:

0.450

Gnomad EAS

AF:

0.275

Gnomad SAS

AF:

0.276

Gnomad FIN

AF:

0.436

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.378

Gnomad OTH

AF:

0.335

GnomAD3 exomes

AF:

0.336

AC:

78478

AN:

233450

Hom.:

13891

AF XY:

0.341

AC XY:

43764

AN XY:

128302

show subpopulations

Gnomad AFR exome

AF:

0.262

Gnomad AMR exome

AF:

0.234

Gnomad ASJ exome

AF:

0.448

Gnomad EAS exome

AF:

0.280

Gnomad SAS exome

AF:

0.282

Gnomad FIN exome

AF:

0.429

Gnomad NFE exome

AF:

0.382

Gnomad OTH exome

AF:

0.357

GnomAD4 exome

AF:

0.360

AC:

520248

AN:

1444100

Hom.:

95473

Cov.:

AF XY:

0.360

AC XY:

258706

AN XY:

718794

show subpopulations

Gnomad4 AFR exome

AF:

0.258

Gnomad4 AMR exome

AF:

0.243

Gnomad4 ASJ exome

AF:

0.451

Gnomad4 EAS exome

AF:

0.277

Gnomad4 SAS exome

AF:

0.280

Gnomad4 FIN exome

AF:

0.418

Gnomad4 NFE exome

AF:

0.373

Gnomad4 OTH exome

AF:

0.352

GnomAD4 genome

AF:

0.335

AC:

50862

AN:

152010

Hom.:

8870

Cov.:

AF XY:

0.333

AC XY:

24723

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.264

Gnomad4 AMR

AF:

0.274

Gnomad4 ASJ

AF:

0.450

Gnomad4 EAS

AF:

0.275

Gnomad4 SAS

AF:

0.276

Gnomad4 FIN

AF:

0.436

Gnomad4 NFE

AF:

0.378

Gnomad4 OTH

AF:

0.334

Alfa

AF:

0.369

Hom.:

2102

Bravo

AF:

0.321

TwinsUK

AF:

0.385

AC:

1426

ALSPAC

AF:

0.369

AC:

1421

ESP6500AA

AF:

0.269

AC:

737

ESP6500EA

AF:

0.361

AC:

1670

ExAC

AF:

0.338

AC:

38777

Asia WGS

AF:

0.263

AC:

915

AN:

3478

EpiCase

AF:

0.379

EpiControl

AF:

0.383

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.24

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.53

CADD

Benign

DANN

Benign

0.96

DEOGEN2

Benign

0.050

.;T

Eigen

Benign

-0.38

Eigen_PC

Benign

-0.43

FATHMM_MKL

Uncertain

0.89

LIST_S2

Benign

0.75

T;T

MetaRNN

Benign

0.013

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.7

.;L

PrimateAI

Uncertain

0.74

PROVEAN

Uncertain

-2.9

.;D

REVEL

Benign

0.18

Sift

Benign

0.081

.;T

Sift4G

Uncertain

0.053

T;T

Polyphen

0.59

.;P

Vest4

0.14

MPC

0.0062

ClinPred

0.036

GERP RS

2.3

Varity_R

0.25

gMVP

0.57

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over