Genetic Variant ENST00000695932.1:n.509+50722G>A (chr2-217044740-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+50722G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,964 control chromosomes in the GnomAD database, including 19,190 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 0.49 ( 19190 hom., cov: 33)

Consequence

TESHL
ENST00000695932.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.156

Publications

15 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 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+50722G>A	intron_variant	Intron 3 of 11
TESHL	ENST00000695934.1 link	n.172+50722G>A	intron_variant	Intron 3 of 8
TESHL	ENST00000695937.1 link	n.289+7460G>A	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.492

AC:

74648

AN:

151844

Hom.:

19166

Cov.:

show subpopulations

Gnomad AFR

AF:

0.393

Gnomad AMI

AF:

0.402

Gnomad AMR

AF:

0.599

Gnomad ASJ

AF:

0.467

Gnomad EAS

AF:

0.902

Gnomad SAS

AF:

0.489

Gnomad FIN

AF:

0.484

Gnomad MID

AF:

0.386

Gnomad NFE

AF:

0.500

Gnomad OTH

AF:

0.501

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

GnomAD4 genome

AF:

0.492

AC:

74714

AN:

151964

Hom.:

19190

Cov.:

AF XY:

0.493

AC XY:

36633

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.393

AC:

16263

AN:

41426

American (AMR)

AF:

0.600

AC:

9153

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.467

AC:

1622

AN:

3472

East Asian (EAS)

AF:

0.901

AC:

4657

AN:

5166

South Asian (SAS)

AF:

0.490

AC:

2359

AN:

4818

European-Finnish (FIN)

AF:

0.484

AC:

5103

AN:

10544

Middle Eastern (MID)

AF:

0.384

AC:

113

AN:

294

European-Non Finnish (NFE)

AF:

0.500

AC:

34006

AN:

67960

Other (OTH)

AF:

0.508

AC:

1071

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1892

3785

5677

7570

9462

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

678

1356

2034

2712

3390

<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:

0.489

Hom.:

15539

Bravo

AF:

0.500

Asia WGS

AF:

0.726

AC:

2521

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.38

(source)

DANN

Benign

0.37

PhyloP100

0.16

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