12-114359288-G-T

Variant summary

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

The NM_181486.4(TBX5):c.983-3182C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 151,962 control chromosomes in the GnomAD database, including 33,342 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 0.66 (33342 hom., cov: 32)
• Consequence: TBX5 NM_181486.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21

Genes affected

TBX5 (HGNC:11604): (T-box transcription factor 5) 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. This gene is closely linked to related family member T-box 3 (ulnar mammary syndrome) on human chromosome 12. The encoded protein may play a role in heart development and specification of limb identity. Mutations in this gene have been associated with Holt-Oram syndrome, a developmental disorder affecting the heart and upper limbs. Several transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBX5	NM_181486.4	c.983-3182C>A		intron_variant		ENST00000405440.7
TBX5	NM_000192.3	c.983-3182C>A		intron_variant
TBX5	NM_080717.4	c.833-3182C>A		intron_variant
TBX5	XM_017019912.2	c.1031-3182C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBX5	ENST00000405440.7	c.983-3182C>A		intron_variant		1	NM_181486.4	P1
TBX5	ENST00000310346.8	c.983-3182C>A		intron_variant		1		P1
TBX5	ENST00000349716.9	c.833-3182C>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99660 AN: 151844 Hom.: 33333 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.656 AC: 99697 AN: 151962 Hom.: 33342 Cov.: 32 AF XY: 0.649 AC XY: 48198 AN XY: 74270

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.640

Alfa AF: 0.700 Hom.: 50133

Bravo AF: 0.641

Asia WGS AF: 0.466 AC: 1622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
Cadd	Benign	16
Dann	Benign	0.83

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: rs10507248; hg19: chr12-114797093;