X-72159919-C-T

Position:

• chrX-72159919-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The ENST00000432517.1(TPT1P15):​n.75C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000394 in 1,190,297 control chromosomes in the GnomAD database, including 1 homozygotes. There are 141 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00029 (1 hom., 4 hem., cov: 24)
  • Exomes 𝑓: 0.00041 (0 hom. 137 hem.)
• Consequence: TPT1P15 ENST00000432517.1 non_coding_transcript_exon
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.915

Genes affected

TPT1P15 (HGNC:55881): (TPT1 pseudogene 15)

NHSL2 (HGNC:33737): (NHS like 2) Predicted to enable calcium ion binding activity. Predicted to be involved in cell differentiation. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BP6: Variant X-72159919-C-T is Benign according to our data. Variant chrX-72159919-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2660906.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Hemizygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TPT1P15	ENST00000432517.1	n.75C>T		non_coding_transcript_exon_variant	1/1
NHSL2	ENST00000623354.1	n.438C>T		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.000286 AC: 32 AN: 112081 Hom.: 1 Cov.: 24 AF XY: 0.000117 AC XY: 4 AN XY: 34259

Gnomad AFR AF: 0.000291

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00264

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000300

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000430 AC: 78 AN: 181529 Hom.: 0 AF XY: 0.000448 AC XY: 30 AN XY: 66945

Gnomad AFR exome AF: 0.000321

Gnomad AMR exome AF: 0.0000366

Gnomad ASJ exome AF: 0.00565

Gnomad EAS exome AF: 0.000145

Gnomad SAS exome AF: 0.000106

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000295

Gnomad OTH exome AF: 0.000675

GnomAD4 exome AF: 0.000405 AC: 437 AN: 1078216 Hom.: 0 Cov.: 32 AF XY: 0.000389 AC XY: 137 AN XY: 352132

Gnomad4 AFR exome AF: 0.000269

Gnomad4 AMR exome AF: 0.0000290

Gnomad4 ASJ exome AF: 0.00492

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000557

Gnomad4 FIN exome AF: 0.0000260

Gnomad4 NFE exome AF: 0.000369

Gnomad4 OTH exome AF: 0.000583

GnomAD4 genome AF: 0.000286 AC: 32 AN: 112081 Hom.: 1 Cov.: 24 AF XY: 0.000117 AC XY: 4 AN XY: 34259

Gnomad4 AFR AF: 0.000291

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00264

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000300

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000998 Hom.: 7

Bravo AF: 0.000336

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jun 01, 2022

FLJ44635: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.2
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs201014184; hg19: chrX-71379769;