Genetic Variant TESHL:n.389-1182A>G (chr2-216763707-A-G) – 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.389-1182A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 152,028 control chromosomes in the GnomAD database, including 32,644 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 0.65 ( 32644 hom., cov: 32)

Consequence

TESHL
ENST00000447289.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0150

Publications

11 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=-0.94).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGFBP-AS1	NR_187138.1 link	n.407-1182A>G		intron_variant	Intron 2 of 5
IGFBP-AS1	NR_187139.1 link	n.407-1182A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TESHL	ENST00000447289.1 link	n.389-1182A>G	intron_variant	Intron 2 of 3	5
TESHL	ENST00000695932.1 link	n.448+51238A>G	intron_variant	Intron 2 of 11
TESHL	ENST00000695934.1 link	n.111+51238A>G	intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes

AF:

0.647

AC:

98284

AN:

151910

Hom.:

32625

Cov.:

show subpopulations

Gnomad AFR

AF:

0.509

Gnomad AMI

AF:

0.704

Gnomad AMR

AF:

0.623

Gnomad ASJ

AF:

0.760

Gnomad EAS

AF:

0.524

Gnomad SAS

AF:

0.704

Gnomad FIN

AF:

0.626

Gnomad MID

AF:

0.725

Gnomad NFE

AF:

0.737

Gnomad OTH

AF:

0.685

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

GnomAD4 genome

AF:

0.647

AC:

98336

AN:

152028

Hom.:

32644

Cov.:

AF XY:

0.642

AC XY:

47692

AN XY:

74280

show subpopulations

African (AFR)

AF:

0.509

AC:

21070

AN:

41426

American (AMR)

AF:

0.623

AC:

9518

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.760

AC:

2638

AN:

3470

East Asian (EAS)

AF:

0.524

AC:

2710

AN:

5172

South Asian (SAS)

AF:

0.705

AC:

3388

AN:

4808

European-Finnish (FIN)

AF:

0.626

AC:

6609

AN:

10560

Middle Eastern (MID)

AF:

0.728

AC:

214

AN:

294

European-Non Finnish (NFE)

AF:

0.737

AC:

50093

AN:

67992

Other (OTH)

AF:

0.690

AC:

1455

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1713

3427

5140

6854

8567

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.713

Hom.:

44237

Bravo

AF:

0.639

Asia WGS

AF:

0.654

AC:

2275

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

2.4

(source)

DANN

Benign

0.52

PhyloP100

0.015

Splicing

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

Publications

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2-216763707-A-G

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