dbSNP rs1882421: TESHL:n.511-8264T>C (chr2-216985694-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 ENST00000447289.1(TESHL):n.511-8264T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,132 control chromosomes in the GnomAD database, including 14,882 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 0.39 ( 14882 hom., cov: 33)

Consequence

TESHL
ENST00000447289.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.135

Publications

1 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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TESHL	ENST00000447289.1 link	n.511-8264T>C	intron_variant	Intron 3 of 3	5
TESHL	ENST00000607591.1 link	n.272+3565T>C	intron_variant	Intron 2 of 2	3
TESHL	ENST00000695932.1 link	n.449-8264T>C	intron_variant	Intron 2 of 11

Frequencies

GnomAD3 genomes

AF:

0.386

AC:

58613

AN:

152016

Hom.:

14840

Cov.:

show subpopulations

Gnomad AFR

AF:

0.723

Gnomad AMI

AF:

0.437

Gnomad AMR

AF:

0.241

Gnomad ASJ

AF:

0.247

Gnomad EAS

AF:

0.0538

Gnomad SAS

AF:

0.280

Gnomad FIN

AF:

0.324

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.263

Gnomad OTH

AF:

0.351

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

GnomAD4 genome

AF:

0.386

AC:

58689

AN:

152132

Hom.:

14882

Cov.:

AF XY:

0.383

AC XY:

28469

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.723

AC:

30019

AN:

41494

American (AMR)

AF:

0.241

AC:

3681

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.247

AC:

858

AN:

3468

East Asian (EAS)

AF:

0.0534

AC:

276

AN:

5170

South Asian (SAS)

AF:

0.279

AC:

1344

AN:

4816

European-Finnish (FIN)

AF:

0.324

AC:

3432

AN:

10588

Middle Eastern (MID)

AF:

0.337

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.263

AC:

17852

AN:

67980

Other (OTH)

AF:

0.346

AC:

730

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1537

3075

4612

6150

7687

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

508

1016

1524

2032

2540

<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:

0.292

Hom.:

15973

Bravo

AF:

0.391

Asia WGS

AF:

0.185

AC:

646

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

7.1

(source)

DANN

Benign

0.44

PhyloP100

0.14

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