Variant chr1-109075949-C-T 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 ENST00000338366.6(TAF13):c.-2G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00243 in 1,614,206 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0022 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0025 ( 25 hom. )

Consequence

TAF13
ENST00000338366.6 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0570

Variant links:

Genes affected

TAF13 (HGNC:11546): (TATA-box binding protein associated factor 13) Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein that coordinates these activities is transcription factor IID (TFIID), which binds to the core promoter to position the polymerase properly, serves as the scaffold for assembly of the remainder of the transcription complex, and acts as a channel for regulatory signals. TFIID is composed of the TATA-binding protein (TBP) and a group of evolutionarily conserved proteins known as TBP-associated factors or TAFs. TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors (GTFs) to facilitate complex assembly and transcription initiation. This gene encodes a small subunit associated with a subset of TFIID complexes. This subunit interacts with TBP and with two other small subunits of TFIID, TAF10 and TAF11. There is a pseudogene located on chromosome 6. [provided by RefSeq, Jul 2008]

TAF13 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 1-109075949-C-T is Benign according to our data. Variant chr1-109075949-C-T is described in ClinVar as [Benign]. Clinvar id is 2585673.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAdExome4 at 25 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAF13	NM_005645.4 linkuse as main transcript	c.-2G>A		5_prime_UTR_variant	1/4	ENST00000338366.6	NP_005636.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
TAF13	ENST00000338366.6 linkuse as main transcript	c.-2G>A	5_prime_UTR_variant	1/4	1	NM_005645.4	ENSP00000355051	P1
TAF13	ENST00000461096.7 linkuse as main transcript	c.-291G>A	5_prime_UTR_variant	1/4	5		ENSP00000433883
TAF13	ENST00000692048.1 linkuse as main transcript	c.-2G>A	5_prime_UTR_variant	1/5			ENSP00000508876

Frequencies

GnomAD3 genomes

AF:

0.00221

AC:

336

AN:

152220

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000217

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00353

Gnomad ASJ

AF:

0.0202

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0106

Gnomad FIN

AF:

0.0000942

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00204

Gnomad OTH

AF:

0.00430

GnomAD3 exomes

AF:

0.00402

AC:

1011

AN:

251416

Hom.:

AF XY:

0.00474

AC XY:

644

AN XY:

135894

show subpopulations

Gnomad AFR exome

AF:

0.000185

Gnomad AMR exome

AF:

0.00249

Gnomad ASJ exome

AF:

0.0249

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0121

Gnomad FIN exome

AF:

0.0000462

Gnomad NFE exome

AF:

0.00243

Gnomad OTH exome

AF:

0.00391

GnomAD4 exome

AF:

0.00245

AC:

3582

AN:

1461868

Hom.:

Cov.:

AF XY:

0.00283

AC XY:

2061

AN XY:

727230

show subpopulations

Gnomad4 AFR exome

AF:

0.000269

Gnomad4 AMR exome

AF:

0.00268

Gnomad4 ASJ exome

AF:

0.0239

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0118

Gnomad4 FIN exome

AF:

0.000112

Gnomad4 NFE exome

AF:

0.00131

Gnomad4 OTH exome

AF:

0.00422

GnomAD4 genome

AF:

0.00221

AC:

337

AN:

152338

Hom.:

Cov.:

AF XY:

0.00221

AC XY:

165

AN XY:

74498

show subpopulations

Gnomad4 AFR

AF:

0.000216

Gnomad4 AMR

AF:

0.00353

Gnomad4 ASJ

AF:

0.0202

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0108

Gnomad4 FIN

AF:

0.0000942

Gnomad4 NFE

AF:

0.00204

Gnomad4 OTH

AF:

0.00426

Alfa

AF:

0.00312

Hom.:

Bravo

AF:

0.00216

Asia WGS

AF:

0.00462

AC:

AN:

3478

EpiCase

AF:

0.00284

EpiControl

AF:

0.00367

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Intellectual disability, autosomal recessive 60

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2024

TAF13: BP4, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

9.2

DANN

Benign

0.84

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over