Variant 10-101089612-CT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NR_130723.1(TLX1NB):n.1590del 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 0.00712 in 1,330,744 control chromosomes in the GnomAD database, including 46 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0051 ( 4 hom., cov: 33)

Exomes 𝑓: 0.0074 ( 42 hom. )

Consequence

TLX1NB
NR_130723.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.391

Variant links:

Genes affected

TLX1NB (HGNC:37183): (TLX1 neighbor)

TLX1NB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 10-101089612-CT-C is Benign according to our data. Variant chr10-101089612-CT-C is described in ClinVar as [Likely_benign]. Clinvar id is 2640768.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TLX1NB	NR_130723.1 linkuse as main transcript	n.1590del		non_coding_transcript_exon_variant	3/3
TLX1NB	NR_130722.1 linkuse as main transcript	n.1619del		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TLX1NB	ENST00000445873.5 linkuse as main transcript	n.1570del		non_coding_transcript_exon_variant	3/3	1

Frequencies

GnomAD3 genomes

AF:

0.00512

AC:

780

AN:

152200

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00142

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.00583

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000828

Gnomad FIN

AF:

0.00499

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00792

Gnomad OTH

AF:

0.00573

GnomAD3 exomes

AF:

0.00468

AC:

891

AN:

190462

Hom.:

AF XY:

0.00471

AC XY:

480

AN XY:

101916

show subpopulations

Gnomad AFR exome

AF:

0.00109

Gnomad AMR exome

AF:

0.00309

Gnomad ASJ exome

AF:

0.000222

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000691

Gnomad FIN exome

AF:

0.00542

Gnomad NFE exome

AF:

0.00804

Gnomad OTH exome

AF:

0.00417

GnomAD4 exome

AF:

0.00738

AC:

8694

AN:

1178426

Hom.:

Cov.:

AF XY:

0.00713

AC XY:

4136

AN XY:

580020

show subpopulations

Gnomad4 AFR exome

AF:

0.00129

Gnomad4 AMR exome

AF:

0.00318

Gnomad4 ASJ exome

AF:

0.000247

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000719

Gnomad4 FIN exome

AF:

0.00508

Gnomad4 NFE exome

AF:

0.00865

Gnomad4 OTH exome

AF:

0.00522

GnomAD4 genome

AF:

0.00512

AC:

780

AN:

152318

Hom.:

Cov.:

AF XY:

0.00542

AC XY:

404

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.00142

Gnomad4 AMR

AF:

0.00582

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000829

Gnomad4 FIN

AF:

0.00499

Gnomad4 NFE

AF:

0.00792

Gnomad4 OTH

AF:

0.00567

Alfa

AF:

0.00371

Hom.:

Bravo

AF:

0.00476

Asia WGS

AF:

0.000866

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2022

TLX1NB: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over