Genetic Variant TLX1NB:n.1570delA (chr10-101089612-CT-C) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The ENST00000445873.5(TLX1NB):n.1570delA 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
ENST00000445873.5 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.391

Publications

5 publications found

Variant links:

COSMIC-nc: COSV71011919

Genes affected

TLX1NB (HGNC:37183): (TLX1 neighbor)

TLX1NB links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -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 VariationId is 2640768.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445873.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLX1NB	NR_130722.1		n.1619delA		non_coding_transcript_exon	Exon 3 of 3
	TLX1NB	NR_130723.1		n.1590delA		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
TLX1NB	ENST00000445873.5	TSL:1	n.1570delA	non_coding_transcript_exon	Exon 3 of 3
TLX1NB	ENST00000747503.1		n.1960delA	non_coding_transcript_exon	Exon 3 of 3
TLX1NB	ENST00000747504.1		n.1720delA	non_coding_transcript_exon	Exon 4 of 4

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

GnomAD2 exomes

AF:

0.00468

AC:

891

AN:

190462

AF XY:

0.00471

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 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

African (AFR)

AF:

0.00129

AC:

AN:

25668

American (AMR)

AF:

0.00318

AC:

AN:

30854

Ashkenazi Jewish (ASJ)

AF:

0.000247

AC:

AN:

16198

East Asian (EAS)

AF:

0.00

AC:

AN:

15224

South Asian (SAS)

AF:

0.000719

AC:

AN:

77874

European-Finnish (FIN)

AF:

0.00508

AC:

154

AN:

30312

Middle Eastern (MID)

AF:

0.00905

AC:

AN:

4422

European-Non Finnish (NFE)

AF:

0.00865

AC:

8086

AN:

935124

Other (OTH)

AF:

0.00522

AC:

223

AN:

42750

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

502

1004

1506

2008

2510

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

356

712

1068

1424

1780

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00512

AC:

780

AN:

152318

Hom.:

Cov.:

AF XY:

0.00542

AC XY:

404

AN XY:

74484

show subpopulations

African (AFR)

AF:

0.00142

AC:

AN:

41578

American (AMR)

AF:

0.00582

AC:

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.000288

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5168

South Asian (SAS)

AF:

0.000829

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.00499

AC:

AN:

10628

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00792

AC:

539

AN:

68024

Other (OTH)

AF:

0.00567

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

109

146

182

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00371

Hom.:

Bravo

AF:

0.00476

Asia WGS

AF:

0.000866

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.39

Mutation Taster

=193/7

polymorphism

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over