Genetic Variant TESHL:n.509+49731A>G (chr2-217043749-A-G) – 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+49731A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,062 control chromosomes in the GnomAD database, including 12,718 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 0.40 ( 12718 hom., cov: 32)

Consequence

TESHL
ENST00000695932.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.229

Publications

9 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 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+49731A>G	intron_variant	Intron 3 of 11
TESHL	ENST00000695934.1 link	n.172+49731A>G	intron_variant	Intron 3 of 8
TESHL	ENST00000695937.1 link	n.289+6469A>G	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.401

AC:

60993

AN:

151944

Hom.:

12705

Cov.:

show subpopulations

Gnomad AFR

AF:

0.471

Gnomad AMI

AF:

0.439

Gnomad AMR

AF:

0.332

Gnomad ASJ

AF:

0.461

Gnomad EAS

AF:

0.102

Gnomad SAS

AF:

0.378

Gnomad FIN

AF:

0.294

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.412

Gnomad OTH

AF:

0.401

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

GnomAD4 genome

AF:

0.401

AC:

61048

AN:

152062

Hom.:

12718

Cov.:

AF XY:

0.392

AC XY:

29132

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.471

AC:

19526

AN:

41476

American (AMR)

AF:

0.332

AC:

5073

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.461

AC:

1600

AN:

3472

East Asian (EAS)

AF:

0.102

AC:

529

AN:

5188

South Asian (SAS)

AF:

0.379

AC:

1827

AN:

4818

European-Finnish (FIN)

AF:

0.294

AC:

3104

AN:

10560

Middle Eastern (MID)

AF:

0.480

AC:

141

AN:

294

European-Non Finnish (NFE)

AF:

0.412

AC:

27997

AN:

67954

Other (OTH)

AF:

0.404

AC:

852

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1840

3680

5521

7361

9201

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.400

Hom.:

24010

Bravo

AF:

0.406

Asia WGS

AF:

0.248

AC:

862

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.49

(source)

DANN

Benign

0.53

PhyloP100

-0.23

Splicing

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

Publications

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2-217043749-A-G

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