1-118884605-GAAA-G

Position:

• chr1-118884605-GAAA-G

Variant summary

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

The NM_001330677.2(TBX15):​c.*124_*126delTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00867 in 762,952 control chromosomes in the GnomAD database, including 91 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.033 (86 hom., cov: 27)
  • Exomes 𝑓: 0.0058 (5 hom.)
• Consequence: TBX15 NM_001330677.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.818

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-GAAA-G is Benign according to our data. Variant chr1-118884605-GAAA-G is described in ClinVar as [Benign]. Clinvar id is 1251229.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBX15	NM_001330677.2	c.*124_*126delTTT		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.*124_*126delTTT		3_prime_UTR_variant	8/8	5	NM_001330677.2	ENSP00000358437.3
TBX15	ENST00000207157	c.*124_*126delTTT		3_prime_UTR_variant	8/8	1		ENSP00000207157.3
TBX15	ENST00000449873	c.*124_*126delTTT		3_prime_UTR_variant	4/4	5		ENSP00000398625.1

Frequencies

GnomAD3 genomes AF: 0.0329 AC: 2659 AN: 80732 Hom.: 86 Cov.: 27

Gnomad AFR AF: 0.0925

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0150

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00276

Gnomad SAS AF: 0.00150

Gnomad FIN AF: 0.000315

Gnomad MID AF: 0.00833

Gnomad NFE AF: 0.000223

Gnomad OTH AF: 0.0229

GnomAD4 exome AF: 0.00580 AC: 3955 AN: 682200 Hom.: 5 AF XY: 0.00563 AC XY: 1965 AN XY: 349106

Gnomad4 AFR exome AF: 0.0593

Gnomad4 AMR exome AF: 0.00839

Gnomad4 ASJ exome AF: 0.00433

Gnomad4 EAS exome AF: 0.00604

Gnomad4 SAS exome AF: 0.00229

Gnomad4 FIN exome AF: 0.00449

Gnomad4 NFE exome AF: 0.00416

Gnomad4 OTH exome AF: 0.00940

GnomAD4 genome AF: 0.0329 AC: 2660 AN: 80752 Hom.: 86 Cov.: 27 AF XY: 0.0341 AC XY: 1289 AN XY: 37844

Gnomad4 AFR AF: 0.0924

Gnomad4 AMR AF: 0.0150

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00276

Gnomad4 SAS AF: 0.00149

Gnomad4 FIN AF: 0.000315

Gnomad4 NFE AF: 0.000223

Gnomad4 OTH AF: 0.0229

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

Sep 13, 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;