rs2142333

chr8-115647231-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014112.5(TRPS1):c.-122+21314G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,776 control chromosomes in the GnomAD database, including 17,876 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.46 (17876 hom., cov: 32)
• Consequence: TRPS1 NM_014112.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

Genes affected

TRPS1 (HGNC:12340): (transcriptional repressor GATA binding 1) This gene encodes a transcription factor that represses GATA-regulated genes and binds to a dynein light chain protein. Binding of the encoded protein to the dynein light chain protein affects binding to GATA consensus sequences and suppresses its transcriptional activity. Defects in this gene are a cause of tricho-rhino-phalangeal syndrome (TRPS) types I-III. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPS1	NM_014112.5	c.-122+21314G>A		intron_variant		ENST00000395715.8
TRPS1	NM_001282902.3	c.10+20643G>A		intron_variant
TRPS1	NM_001282903.3	c.-129+21314G>A		intron_variant
TRPS1	NM_001330599.2	c.-3+21314G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPS1	ENST00000395715.8	c.-122+21314G>A		intron_variant		1	NM_014112.5	A1

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69324 AN: 151656 Hom.: 17846 Cov.: 32

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.276

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.392

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.457 AC: 69409 AN: 151776 Hom.: 17876 Cov.: 32 AF XY: 0.462 AC XY: 34253 AN XY: 74144

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.394

Alfa AF: 0.401 Hom.: 1723

Bravo AF: 0.470

Asia WGS AF: 0.416 AC: 1447 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.7
Dann	Benign	0.45

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: rs2142333; hg19: chr8-116659458;