NM_001330677.2:c.*121_*126delTTTTTT

Variant names:

• chr1-118884605-GAAAAAA-G
• rs536044359
• NM_001330677.2:c.*121_*126delTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001330677.2(TBX15):​c.*121_*126delTTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000987 in 769,840 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000050 (0 hom., cov: 27)
  • Exomes 𝑓: 0.00010 (0 hom.)
• Consequence: TBX15 NM_001330677.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.33
• Publications: 0 publications found

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]

TBX15 Gene-Disease associations (from GenCC):

• pelviscapular dysplasia

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBX15	NM_001330677.2	c.*121_*126delTTTTTT		3_prime_UTR_variant	Exon 8 of 8	ENST00000369429.5	NP_001317606.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBX15	ENST00000369429.5	c.*121_*126delTTTTTT		3_prime_UTR_variant	Exon 8 of 8	5	NM_001330677.2	ENSP00000358437.3
TBX15	ENST00000207157.7	c.*121_*126delTTTTTT		3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000207157.3
TBX15	ENST00000449873.5	c.*121_*126delTTTTTT		3_prime_UTR_variant	Exon 4 of 4	5		ENSP00000398625.1

Frequencies

GnomAD3 genomes AF: 0.0000495 AC: 4 AN: 80754 Hom.: 0 Cov.: 27

Gnomad AFR AF: 0.0000368

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000499

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000558

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000104 AC: 72 AN: 689086 Hom.: 0 AF XY: 0.000102 AC XY: 36 AN XY: 352720

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000611 AC: 1 AN: 16362

American (AMR) AF: 0.000106 AC: 2 AN: 18860

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14710

East Asian (EAS) AF: 0.000101 AC: 3 AN: 29734

South Asian (SAS) AF: 0.0000613 AC: 3 AN: 48914

European-Finnish (FIN) AF: 0.0000693 AC: 2 AN: 28854

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2334

European-Non Finnish (NFE) AF: 0.000119 AC: 59 AN: 496528

Other (OTH) AF: 0.0000610 AC: 2 AN: 32790

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.0000495 AC: 4 AN: 80754 Hom.: 0 Cov.: 27 AF XY: 0.0000793 AC XY: 3 AN XY: 37834

African (AFR) AF: 0.0000368 AC: 1 AN: 27202

American (AMR) AF: 0.00 AC: 0 AN: 6812

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1932

East Asian (EAS) AF: 0.00 AC: 0 AN: 2172

South Asian (SAS) AF: 0.000499 AC: 1 AN: 2006

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3174

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 120

European-Non Finnish (NFE) AF: 0.0000558 AC: 2 AN: 35834

Other (OTH) AF: 0.00 AC: 0 AN: 1094

Alfa AF: 0.00 Hom.: 6

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs536044359; hg19: chr1-119427228;