Variant 1-222563156-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005681.4(TAF1A):c.1085+17G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 1,580,354 control chromosomes in the GnomAD database, including 20,587 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.21 ( 4515 hom., cov: 32)

Exomes 𝑓: 0.14 ( 16072 hom. )

Consequence

TAF1A
NM_005681.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.92

Variant links:

Genes affected

TAF1A (HGNC:11532): (TATA-box binding protein associated factor, RNA polymerase I subunit A) This gene encodes a subunit of the RNA polymerase I complex, Selectivity Factor I (SLI). The encoded protein is a TATA box-binding protein-associated factor that plays a role in the assembly of the RNA polymerase I preinitiation complex. Alternate splicing results in multiple transcript variants encoding multiple isoforms.[provided by RefSeq, Jan 2011]

TAF1A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP6

Variant 1-222563156-C-T is Benign according to our data. Variant chr1-222563156-C-T is described in ClinVar as [Benign]. Clinvar id is 1182797.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAF1A	NM_005681.4 linkuse as main transcript	c.1085+17G>A		intron_variant		ENST00000352967.9	NP_005672.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
TAF1A	ENST00000352967.9 linkuse as main transcript	c.1085+17G>A	intron_variant	1	NM_005681.4	ENSP00000327072	P1	Q15573-1
TAF1A	ENST00000350027.8 linkuse as main transcript	c.1085+17G>A	intron_variant	2		ENSP00000339976	P1	Q15573-1
TAF1A	ENST00000366890.5 linkuse as main transcript	c.743+17G>A	intron_variant	2		ENSP00000355856		Q15573-2

Frequencies

GnomAD3 genomes

AF:

0.212

AC:

32128

AN:

151824

Hom.:

4501

Cov.:

show subpopulations

Gnomad AFR

AF:

0.408

Gnomad AMI

AF:

0.155

Gnomad AMR

AF:

0.124

Gnomad ASJ

AF:

0.103

Gnomad EAS

AF:

0.145

Gnomad SAS

AF:

0.0905

Gnomad FIN

AF:

0.177

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.139

Gnomad OTH

AF:

0.174

GnomAD3 exomes

AF:

0.145

AC:

34952

AN:

240304

Hom.:

3270

AF XY:

0.139

AC XY:

18136

AN XY:

130486

show subpopulations

Gnomad AFR exome

AF:

0.415

Gnomad AMR exome

AF:

0.0780

Gnomad ASJ exome

AF:

0.100

Gnomad EAS exome

AF:

0.148

Gnomad SAS exome

AF:

0.0937

Gnomad FIN exome

AF:

0.173

Gnomad NFE exome

AF:

0.138

Gnomad OTH exome

AF:

0.138

GnomAD4 exome

AF:

0.141

AC:

201842

AN:

1428412

Hom.:

16072

Cov.:

AF XY:

0.139

AC XY:

98981

AN XY:

711904

show subpopulations

Gnomad4 AFR exome

AF:

0.420

Gnomad4 AMR exome

AF:

0.0829

Gnomad4 ASJ exome

AF:

0.0990

Gnomad4 EAS exome

AF:

0.141

Gnomad4 SAS exome

AF:

0.0961

Gnomad4 FIN exome

AF:

0.177

Gnomad4 NFE exome

AF:

0.138

Gnomad4 OTH exome

AF:

0.147

GnomAD4 genome

AF:

0.212

AC:

32186

AN:

151942

Hom.:

4515

Cov.:

AF XY:

0.209

AC XY:

15522

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.408

Gnomad4 AMR

AF:

0.123

Gnomad4 ASJ

AF:

0.103

Gnomad4 EAS

AF:

0.145

Gnomad4 SAS

AF:

0.0899

Gnomad4 FIN

AF:

0.177

Gnomad4 NFE

AF:

0.139

Gnomad4 OTH

AF:

0.175

Alfa

AF:

0.165

Hom.:

527

Bravo

AF:

0.219

Asia WGS

AF:

0.125

AC:

432

AN:

3472

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 24, 2020	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.018

DANN

Benign

0.35

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