Genetic Variant TESHL:n.509+36015T>C (chr2-217030033-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000695932.1(TESHL):n.509+36015T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,956 control chromosomes in the GnomAD database, including 9,901 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 0.34 ( 9901 hom., cov: 32)

Consequence

TESHL
ENST00000695932.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0800

Publications

17 publications found

Variant links:

Genes affected

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

TESHL 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
TESHL	ENST00000695932.1 link	n.509+36015T>C	intron_variant	Intron 3 of 11
TESHL	ENST00000695934.1 link	n.172+36015T>C	intron_variant	Intron 3 of 8
TESHL	ENST00000695937.1 link	n.222-7180T>C	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.341

AC:

51776

AN:

151838

Hom.:

9885

Cov.:

show subpopulations

Gnomad AFR

AF:

0.349

Gnomad AMI

AF:

0.199

Gnomad AMR

AF:

0.427

Gnomad ASJ

AF:

0.246

Gnomad EAS

AF:

0.856

Gnomad SAS

AF:

0.340

Gnomad FIN

AF:

0.352

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.283

Gnomad OTH

AF:

0.337

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

GnomAD4 genome

AF:

0.341

AC:

51828

AN:

151956

Hom.:

9901

Cov.:

AF XY:

0.348

AC XY:

25833

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.349

AC:

14467

AN:

41406

American (AMR)

AF:

0.428

AC:

6542

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.246

AC:

853

AN:

3466

East Asian (EAS)

AF:

0.856

AC:

4419

AN:

5162

South Asian (SAS)

AF:

0.340

AC:

1632

AN:

4806

European-Finnish (FIN)

AF:

0.352

AC:

3717

AN:

10568

Middle Eastern (MID)

AF:

0.221

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.283

AC:

19238

AN:

67950

Other (OTH)

AF:

0.338

AC:

714

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1655

3310

4964

6619

8274

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

492

984

1476

1968

2460

<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:

0.302

Hom.:

32403

Bravo

AF:

0.354

Asia WGS

AF:

0.614

AC:

2131

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.4

(source)

DANN

Benign

0.47

PhyloP100

0.080

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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