1-118884605-G-GA

Position:

• chr1-118884605-G-GA

Variant summary

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

The NM_001330677.2(TBX15):​c.*126dupT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 749,066 control chromosomes in the GnomAD database, including 490 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.11 (468 hom., cov: 27)
  • Exomes 𝑓: 0.28 (22 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-G-GA is Benign according to our data. Variant chr1-118884605-G-GA is described in ClinVar as [Benign]. Clinvar id is 1297885.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBX15	NM_001330677.2	c.*126dupT		3_prime_UTR_variant	8/8	ENST00000369429.5	NP_001317606.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TBX15	ENST00000369429	c.*126dupT		3_prime_UTR_variant	8/8	5	NM_001330677.2	ENSP00000358437.3
TBX15	ENST00000207157	c.*126dupT		3_prime_UTR_variant	8/8	1		ENSP00000207157.3
TBX15	ENST00000449873	c.*126dupT		3_prime_UTR_variant	4/4	5		ENSP00000398625.1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 8867 AN: 80604 Hom.: 469 Cov.: 27

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.0764

Gnomad AMR AF: 0.0981

Gnomad ASJ AF: 0.0820

Gnomad EAS AF: 0.0268

Gnomad SAS AF: 0.0544

Gnomad FIN AF: 0.0438

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.0749

Gnomad OTH AF: 0.117

GnomAD4 exome AF: 0.280 AC: 187466 AN: 668442 Hom.: 22 Cov.: 6 AF XY: 0.281 AC XY: 95928 AN XY: 341640

Gnomad4 AFR exome AF: 0.233

Gnomad4 AMR exome AF: 0.289

Gnomad4 ASJ exome AF: 0.280

Gnomad4 EAS exome AF: 0.291

Gnomad4 SAS exome AF: 0.288

Gnomad4 FIN exome AF: 0.262

Gnomad4 NFE exome AF: 0.281

Gnomad4 OTH exome AF: 0.282

GnomAD4 genome AF: 0.110 AC: 8864 AN: 80624 Hom.: 468 Cov.: 27 AF XY: 0.110 AC XY: 4169 AN XY: 37788

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.0979

Gnomad4 ASJ AF: 0.0820

Gnomad4 EAS AF: 0.0268

Gnomad4 SAS AF: 0.0532

Gnomad4 FIN AF: 0.0438

Gnomad4 NFE AF: 0.0749

Gnomad4 OTH AF: 0.118

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

Aug 15, 2019

- -

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;