rs8060511

Positions:

• chr16-30090275-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004608.4(TBX6):​c.353+483G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,960 control chromosomes in the GnomAD database, including 19,896 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.50 (19896 hom., cov: 31)
• Consequence: TBX6 NM_004608.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBX6	NM_004608.4	c.353+483G>T		intron_variant		ENST00000395224.7
TBX6	XM_011545926.4	c.353+483G>T		intron_variant
TBX6	XM_047434551.1	c.353+483G>T		intron_variant
TBX6	XR_007064904.1	n.476+483G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBX6	ENST00000395224.7	c.353+483G>T		intron_variant		1	NM_004608.4	P1
TBX6	ENST00000279386.6	c.353+483G>T		intron_variant		1		P1
TBX6	ENST00000553607.1	c.353+483G>T		intron_variant		1
TBX6	ENST00000567664.5	c.353+483G>T		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76530 AN: 151842 Hom.: 19870 Cov.: 31

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.481

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.504 AC: 76588 AN: 151960 Hom.: 19896 Cov.: 31 AF XY: 0.497 AC XY: 36942 AN XY: 74264

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.476

Alfa AF: 0.495 Hom.: 3045

Bravo AF: 0.508

Asia WGS AF: 0.366 AC: 1277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.46

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

Other links and lift over

dbSNP: rs8060511; hg19: chr16-30101596;