Genetic Variant TESHL:n.509+125919G>A (chr2-217119937-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 ENST00000695932.1(TESHL):n.509+125919G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 151,956 control chromosomes in the GnomAD database, including 10,054 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 0.24 ( 10054 hom., cov: 32)

Consequence

TESHL
ENST00000695932.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0390

Publications

2 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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TESHL	ENST00000695932.1 link	n.509+125919G>A		intron_variant	Intron 3 of 11
TESHL	ENST00000695934.1 link	n.173-33474G>A		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes

AF:

0.243

AC:

36890

AN:

151838

Hom.:

10017

Cov.:

show subpopulations

Gnomad AFR

AF:

0.668

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.209

Gnomad ASJ

AF:

0.0931

Gnomad EAS

AF:

0.271

Gnomad SAS

AF:

0.140

Gnomad FIN

AF:

0.0107

Gnomad MID

AF:

0.121

Gnomad NFE

AF:

0.0464

Gnomad OTH

AF:

0.202

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

GnomAD4 genome

AF:

0.243

AC:

36992

AN:

151956

Hom.:

10054

Cov.:

AF XY:

0.240

AC XY:

17859

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.668

AC:

27673

AN:

41398

American (AMR)

AF:

0.209

AC:

3181

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.0931

AC:

323

AN:

3468

East Asian (EAS)

AF:

0.271

AC:

1399

AN:

5158

South Asian (SAS)

AF:

0.141

AC:

675

AN:

4794

European-Finnish (FIN)

AF:

0.0107

AC:

113

AN:

10588

Middle Eastern (MID)

AF:

0.130

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0464

AC:

3153

AN:

67988

Other (OTH)

AF:

0.201

AC:

425

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

850

1700

2550

3400

4250

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

300

600

900

1200

1500

<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:

0.103

Hom.:

5611

Bravo

AF:

0.277

Asia WGS

AF:

0.221

AC:

769

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

2.0

(source)

DANN

Benign

0.43

PhyloP100

0.039

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