rs536044359

Variant names:

• chr1-118884605-GAAAAAAAAAA-G
• NM_001330677.2:c.*117_*126delTTTTTTTTTT

Your query was ambiguous. Multiple possible variants found:

• chr1-118884605-GAAAAAAAAAA-G
• chr1-118884605-GAAAAAAAAAA-GAA
• chr1-118884605-GAAAAAAAAAA-GAAA
• chr1-118884605-GAAAAAAAAAA-GAAAA
• chr1-118884605-GAAAAAAAAAA-GAAAAA
• chr1-118884605-GAAAAAAAAAA-GAAAAAA
• chr1-118884605-GAAAAAAAAAA-GAAAAAAA
• chr1-118884605-GAAAAAAAAAA-GAAAAAAAA
• chr1-118884605-GAAAAAAAAAA-GAAAAAAAAA
• chr1-118884605-GAAAAAAAAAA-GAAAAAAAAAAA
• chr1-118884605-GAAAAAAAAAA-GAAAAAAAAAAAA
• chr1-118884605-GAAAAAAAAAA-GAAAAAAAAAAAAA
• chr1-118884605-GAAAAAAAAAA-GAAAAAAAAAAAAAA
• chr1-118884605-GAAAAAAAAAA-GAAAAAAAAAAAAAAA
• chr1-118884605-GAAAAAAAAAA-GAAAAAAAAAAAAAAAA
• chr1-118884605-GAAAAAAAAAA-GAAAAAAAAAAAAAAAAA
• chr1-118884605-GAAAAAAAAAA-GAAAAAAAAAAAAAAAAAA
• chr1-118884605-GAAAAAAAAAA-GAAAAAAAAAAAAAAAAAAA
• chr1-118884605-GAAAAAAAAAA-GAAAAAAAAAAAAAAAAAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001330677.2(TBX15):​c.*117_*126delTTTTTTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000145 in 689,256 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: not found (cov: 27)
  • Exomes 𝑓: 0.0000015 (0 hom.)
• Consequence: TBX15 NM_001330677.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.33

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 Uncertain_significance. Variant got 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.*117_*126delTTTTTTTTTT		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	c.*117_*126delTTTTTTTTTT		3_prime_UTR_variant	Exon 8 of 8	5	NM_001330677.2	ENSP00000358437.3
TBX15	ENST00000207157	c.*117_*126delTTTTTTTTTT		3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000207157.3
TBX15	ENST00000449873	c.*117_*126delTTTTTTTTTT		3_prime_UTR_variant	Exon 4 of 4	5		ENSP00000398625.1

Frequencies

GnomAD3 genomes Cov.: 27

GnomAD4 exome AF: 0.00000145 AC: 1 AN: 689256 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 352790

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000336

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-119427228;