Genetic Variant ENST00000447289.1:n.389-5889G>A (chr2-216759000-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000447289.1(TESHL):n.389-5889G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,114 control chromosomes in the GnomAD database, including 2,947 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 0.18 ( 2947 hom., cov: 32)

Consequence

TESHL
ENST00000447289.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.24

Publications

6 publications found

Variant links:

Genes affected

TESHL (HGNC:52740): (testicular germ cell expressed HSF2 interacting lncRNA)

TESHL links:

IGFBP-AS1 (HGNC:55655): (IGFBP5 antisense RNA 1)

IGFBP-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGFBP-AS1	NR_187138.1 link	n.407-5889G>A		intron_variant	Intron 2 of 5
IGFBP-AS1	NR_187139.1 link	n.407-5889G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TESHL	ENST00000447289.1 link	n.389-5889G>A	intron_variant	Intron 2 of 3	5
TESHL	ENST00000695932.1 link	n.448+46531G>A	intron_variant	Intron 2 of 11
TESHL	ENST00000695934.1 link	n.111+46531G>A	intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes

AF:

0.182

AC:

27624

AN:

151996

Hom.:

2935

Cov.:

show subpopulations

Gnomad AFR

AF:

0.279

Gnomad AMI

AF:

0.188

Gnomad AMR

AF:

0.223

Gnomad ASJ

AF:

0.182

Gnomad EAS

AF:

0.292

Gnomad SAS

AF:

0.162

Gnomad FIN

AF:

0.120

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.116

Gnomad OTH

AF:

0.175

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

GnomAD4 genome

AF:

0.182

AC:

27666

AN:

152114

Hom.:

2947

Cov.:

AF XY:

0.184

AC XY:

13680

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.279

AC:

11574

AN:

41480

American (AMR)

AF:

0.223

AC:

3411

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.182

AC:

631

AN:

3472

East Asian (EAS)

AF:

0.292

AC:

1506

AN:

5154

South Asian (SAS)

AF:

0.161

AC:

779

AN:

4824

European-Finnish (FIN)

AF:

0.120

AC:

1266

AN:

10588

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.116

AC:

7906

AN:

67998

Other (OTH)

AF:

0.172

AC:

363

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1152

2305

3457

4610

5762

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

278

556

834

1112

1390

<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:

0.164

Hom.:

488

Bravo

AF:

0.195

Asia WGS

AF:

0.210

AC:

732

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.46

(source)

DANN

Benign

0.68

PhyloP100

-1.2

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over