Variant 5-134887903-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_024715.4(TXNDC15):c.312A>G(p.Lys104=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 1,614,102 control chromosomes in the GnomAD database, including 17,715 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.12 ( 1341 hom., cov: 33)

Exomes 𝑓: 0.14 ( 16374 hom. )

Consequence

TXNDC15
NM_024715.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.543

Variant links:

Genes affected

TXNDC15 (HGNC:20652): (thioredoxin domain containing 15) This gene encodes a member of the thioredoxin superfamily. Members of this family are characterized by a conserved active motif called the thioredoxin fold that catalyzes disulfide bond formation and isomerization. [provided by RefSeq, Apr 2017]

TXNDC15 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 5-134887903-A-G is Benign according to our data. Variant chr5-134887903-A-G is described in ClinVar as [Benign]. Clinvar id is 1559526.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TXNDC15	NM_024715.4 linkuse as main transcript	c.312A>G	p.Lys104=	synonymous_variant	2/5	ENST00000358387.9	NP_078991.3
TXNDC15	NM_001350735.2 linkuse as main transcript	c.108A>G	p.Lys36=	synonymous_variant	2/5		NP_001337664.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TXNDC15	ENST00000358387.9 linkuse as main transcript	c.312A>G	p.Lys104=	synonymous_variant	2/5	1	NM_024715.4	ENSP00000351157	P1	Q96J42-1

Frequencies

GnomAD3 genomes

AF:

0.122

AC:

18581

AN:

152112

Hom.:

1336

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0549

Gnomad AMI

AF:

0.154

Gnomad AMR

AF:

0.153

Gnomad ASJ

AF:

0.0818

Gnomad EAS

AF:

0.266

Gnomad SAS

AF:

0.196

Gnomad FIN

AF:

0.197

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.130

Gnomad OTH

AF:

0.112

GnomAD3 exomes

AF:

0.151

AC:

37881

AN:

251418

Hom.:

3167

AF XY:

0.152

AC XY:

20696

AN XY:

135884

show subpopulations

Gnomad AFR exome

AF:

0.0535

Gnomad AMR exome

AF:

0.168

Gnomad ASJ exome

AF:

0.0790

Gnomad EAS exome

AF:

0.244

Gnomad SAS exome

AF:

0.193

Gnomad FIN exome

AF:

0.204

Gnomad NFE exome

AF:

0.129

Gnomad OTH exome

AF:

0.151

GnomAD4 exome

AF:

0.143

AC:

208423

AN:

1461872

Hom.:

16374

Cov.:

AF XY:

0.144

AC XY:

104528

AN XY:

727236

show subpopulations

Gnomad4 AFR exome

AF:

0.0507

Gnomad4 AMR exome

AF:

0.168

Gnomad4 ASJ exome

AF:

0.0797

Gnomad4 EAS exome

AF:

0.323

Gnomad4 SAS exome

AF:

0.196

Gnomad4 FIN exome

AF:

0.206

Gnomad4 NFE exome

AF:

0.133

Gnomad4 OTH exome

AF:

0.139

GnomAD4 genome

AF:

0.122

AC:

18599

AN:

152230

Hom.:

1341

Cov.:

AF XY:

0.126

AC XY:

9408

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.0549

Gnomad4 AMR

AF:

0.154

Gnomad4 ASJ

AF:

0.0818

Gnomad4 EAS

AF:

0.266

Gnomad4 SAS

AF:

0.196

Gnomad4 FIN

AF:

0.197

Gnomad4 NFE

AF:

0.130

Gnomad4 OTH

AF:

0.112

Alfa

AF:

0.124

Hom.:

1751

Bravo

AF:

0.116

Asia WGS

AF:

0.224

AC:

776

AN:

3478

EpiCase

AF:

0.124

EpiControl

AF:

0.125

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 29, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

DANN

Benign

0.61

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.34

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.34

Position offset: 0

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