Variant 5-134875367-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_024715.4(TXNDC15):c.103+837G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00683 in 456,276 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0049 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0078 ( 29 hom. )

Consequence

TXNDC15
NM_024715.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.194

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:

LOC124901071 (HGNC:):

LOC124901071 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 5-134875367-G-T is Benign according to our data. Variant chr5-134875367-G-T is described in ClinVar as [Benign]. Clinvar id is 2655711.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00494 (752/152304) while in subpopulation SAS AF= 0.011 (53/4826). AF 95% confidence interval is 0.00862. There are 1 homozygotes in gnomad4. There are 345 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAdExome4 at 29 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
TXNDC15	NM_024715.4 linkuse as main transcript	c.103+837G>T	intron_variant		ENST00000358387.9	NP_078991.3
LOC124901071	XR_007058943.1 linkuse as main transcript	n.32C>A	non_coding_transcript_exon_variant	1/2
TXNDC15	NM_001350735.2 linkuse as main transcript	c.-102+884G>T	intron_variant			NP_001337664.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TXNDC15	ENST00000358387.9 linkuse as main transcript	c.103+837G>T		intron_variant		1	NM_024715.4	ENSP00000351157	P1	Q96J42-1

Frequencies

GnomAD3 genomes

AF:

0.00495

AC:

753

AN:

152186

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00125

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00465

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0112

Gnomad FIN

AF:

0.000471

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00811

Gnomad OTH

AF:

0.00623

GnomAD3 exomes

AF:

0.00669

AC:

859

AN:

128390

Hom.:

AF XY:

0.00720

AC XY:

506

AN XY:

70314

show subpopulations

Gnomad AFR exome

AF:

0.00246

Gnomad AMR exome

AF:

0.00411

Gnomad ASJ exome

AF:

0.000371

Gnomad EAS exome

AF:

0.0000959

Gnomad SAS exome

AF:

0.0126

Gnomad FIN exome

AF:

0.00111

Gnomad NFE exome

AF:

0.00894

Gnomad OTH exome

AF:

0.00650

GnomAD4 exome

AF:

0.00778

AC:

2366

AN:

303972

Hom.:

Cov.:

AF XY:

0.00837

AC XY:

1449

AN XY:

173082

show subpopulations

Gnomad4 AFR exome

AF:

0.00232

Gnomad4 AMR exome

AF:

0.00418

Gnomad4 ASJ exome

AF:

0.000649

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0129

Gnomad4 FIN exome

AF:

0.00113

Gnomad4 NFE exome

AF:

0.00827

Gnomad4 OTH exome

AF:

0.00639

GnomAD4 genome

AF:

0.00494

AC:

752

AN:

152304

Hom.:

Cov.:

AF XY:

0.00463

AC XY:

345

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.00125

Gnomad4 AMR

AF:

0.00464

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0110

Gnomad4 FIN

AF:

0.000471

Gnomad4 NFE

AF:

0.00811

Gnomad4 OTH

AF:

0.00616

Alfa

AF:

0.00554

Hom.:

Bravo

AF:

0.00503

Asia WGS

AF:

0.00318

AC:

AN:

3478

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

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

TXNDC15: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

7.2

DANN

Benign

0.60

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over