dbSNP rs6435957: TESHL:n.509+19468T>C (chr2-217013486-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+19468T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,936 control chromosomes in the GnomAD database, including 17,579 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 0.45 ( 17579 hom., cov: 31)

Consequence

TESHL
ENST00000695932.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.714

Publications

12 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 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+19468T>C	intron_variant	Intron 3 of 11
TESHL	ENST00000695934.1 link	n.172+19468T>C	intron_variant	Intron 3 of 8
TESHL	ENST00000695937.1 link	n.221+19468T>C	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.446

AC:

67737

AN:

151820

Hom.:

17540

Cov.:

show subpopulations

Gnomad AFR

AF:

0.664

Gnomad AMI

AF:

0.237

Gnomad AMR

AF:

0.474

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.886

Gnomad SAS

AF:

0.350

Gnomad FIN

AF:

0.372

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.307

Gnomad OTH

AF:

0.403

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

GnomAD4 genome

AF:

0.446

AC:

67838

AN:

151936

Hom.:

17579

Cov.:

AF XY:

0.448

AC XY:

33307

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.665

AC:

27529

AN:

41412

American (AMR)

AF:

0.475

AC:

7242

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

867

AN:

3472

East Asian (EAS)

AF:

0.886

AC:

4574

AN:

5162

South Asian (SAS)

AF:

0.349

AC:

1678

AN:

4810

European-Finnish (FIN)

AF:

0.372

AC:

3936

AN:

10572

Middle Eastern (MID)

AF:

0.211

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.307

AC:

20887

AN:

67934

Other (OTH)

AF:

0.402

AC:

847

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1669

3339

5008

6678

8347

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

584

1168

1752

2336

2920

<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:

0.352

Hom.:

49531

Bravo

AF:

0.470

Asia WGS

AF:

0.649

AC:

2254

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

0.71

(source)

DANN

Benign

0.73

PhyloP100

-0.71

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