Variant 16-30091481-T-C 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 ENST00000395224.7(TBX6):c.-48-240A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 323,542 control chromosomes in the GnomAD database, including 17,041 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 6425 hom., cov: 30)

Exomes 𝑓: 0.33 ( 10616 hom. )

Consequence

TBX6
ENST00000395224.7 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.604

Variant links:

Genes affected

TBX6 (HGNC:11605): (T-box transcription factor 6) This gene is a member of a phylogenetically conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of developmental processes. Knockout studies in mice indicate that this gene is important for specification of paraxial mesoderm structures. [provided by RefSeq, Aug 2008]

TBX6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BP6

Variant 16-30091481-T-C is Benign according to our data. Variant chr16-30091481-T-C is described in ClinVar as [Benign]. Clinvar id is 427808.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
TBX6	NM_004608.4 linkuse as main transcript	c.-48-240A>G	intron_variant		ENST00000395224.7	NP_004599.2
TBX6	XM_011545926.4 linkuse as main transcript	c.-70A>G	5_prime_UTR_variant	1/9		XP_011544228.1
TBX6	XM_047434551.1 linkuse as main transcript	c.-288A>G	5_prime_UTR_variant	1/8		XP_047290507.1
TBX6	XR_007064904.1 linkuse as main transcript	n.54A>G	non_coding_transcript_exon_variant	1/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TBX6	ENST00000553607.1 linkuse as main transcript	c.-288A>G		5_prime_UTR_variant	1/5	1		ENSP00000461223		O95947-2
TBX6	ENST00000395224.7 linkuse as main transcript	c.-48-240A>G		intron_variant		1	NM_004608.4	ENSP00000378650	P1	O95947-1

Frequencies

GnomAD3 genomes

AF:

0.261

AC:

39385

AN:

150622

Hom.:

6424

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0682

Gnomad AMI

AF:

0.343

Gnomad AMR

AF:

0.287

Gnomad ASJ

AF:

0.315

Gnomad EAS

AF:

0.474

Gnomad SAS

AF:

0.231

Gnomad FIN

AF:

0.404

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.332

Gnomad OTH

AF:

0.276

GnomAD4 exome

AF:

0.331

AC:

57279

AN:

172808

Hom.:

10616

Cov.:

AF XY:

0.327

AC XY:

29253

AN XY:

89520

show subpopulations

Gnomad4 AFR exome

AF:

0.0732

Gnomad4 AMR exome

AF:

0.325

Gnomad4 ASJ exome

AF:

0.294

Gnomad4 EAS exome

AF:

0.584

Gnomad4 SAS exome

AF:

0.229

Gnomad4 FIN exome

AF:

0.405

Gnomad4 NFE exome

AF:

0.327

Gnomad4 OTH exome

AF:

0.300

GnomAD4 genome

AF:

0.261

AC:

39395

AN:

150734

Hom.:

6425

Cov.:

AF XY:

0.264

AC XY:

19436

AN XY:

73526

show subpopulations

Gnomad4 AFR

AF:

0.0682

Gnomad4 AMR

AF:

0.288

Gnomad4 ASJ

AF:

0.315

Gnomad4 EAS

AF:

0.473

Gnomad4 SAS

AF:

0.231

Gnomad4 FIN

AF:

0.404

Gnomad4 NFE

AF:

0.332

Gnomad4 OTH

AF:

0.281

Alfa

AF:

0.308

Hom.:

2929

Bravo

AF:

0.250

Asia WGS

AF:

0.357

AC:

1239

AN:

3478

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	Nov 12, 2018	- -
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

-0.48

CADD

Benign

DANN

Benign

0.90

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