1-118884605-GA-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001330677.2(TBX15):c.*126del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0583 in 762,314 control chromosomes in the GnomAD database, including 47 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.029 (47 hom., cov: 27)
  • Exomes 𝑓: 0.062 (0 hom.)
• Consequence: TBX15 NM_001330677.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.512

Genes affected

TBX15 (HGNC:11594): (T-box transcription factor 15) This gene belongs to the T-box family of genes, which encode a phylogenetically conserved family of transcription factors that regulate a variety of developmental processes. All these genes contain a common T-box DNA-binding domain. Mutations in this gene are associated with Cousin syndrome.[provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-118884605-GA-G is Benign according to our data. Variant chr1-118884605-GA-G is described in ClinVar as [Benign]. Clinvar id is 1243200.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBX15	NM_001330677.2	c.*126del		3_prime_UTR_variant	8/8	ENST00000369429.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBX15	ENST00000369429.5	c.*126del		3_prime_UTR_variant	8/8	5	NM_001330677.2	P1
TBX15	ENST00000207157.7	c.*126del		3_prime_UTR_variant	8/8	1
TBX15	ENST00000449873.5	c.*126del		3_prime_UTR_variant	4/4	5

Frequencies

GnomAD3 genomes AF: 0.0289 AC: 2334 AN: 80746 Hom.: 47 Cov.: 27

Gnomad AFR AF: 0.0729

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0184

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.0124

Gnomad SAS AF: 0.00399

Gnomad FIN AF: 0.00315

Gnomad MID AF: 0.00833

Gnomad NFE AF: 0.00380

Gnomad OTH AF: 0.0219

GnomAD4 exome AF: 0.0617 AC: 42074 AN: 681548 Hom.: 0 Cov.: 6 AF XY: 0.0611 AC XY: 21307 AN XY: 348734

Gnomad4 AFR exome AF: 0.0794

Gnomad4 AMR exome AF: 0.0581

Gnomad4 ASJ exome AF: 0.0629

Gnomad4 EAS exome AF: 0.0762

Gnomad4 SAS exome AF: 0.0430

Gnomad4 FIN exome AF: 0.0604

Gnomad4 NFE exome AF: 0.0621

Gnomad4 OTH exome AF: 0.0648

GnomAD4 genome AF: 0.0289 AC: 2336 AN: 80766 Hom.: 47 Cov.: 27 AF XY: 0.0285 AC XY: 1079 AN XY: 37854

Gnomad4 AFR AF: 0.0729

Gnomad4 AMR AF: 0.0182

Gnomad4 ASJ AF: 0.0109

Gnomad4 EAS AF: 0.0124

Gnomad4 SAS AF: 0.00397

Gnomad4 FIN AF: 0.00315

Gnomad4 NFE AF: 0.00380

Gnomad4 OTH AF: 0.0220

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 22, 2019

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Computational scores

Source: dbNSFP v4.3

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: rs536044359; hg19: chr1-119427228;