dbSNP rs2542197: TESHL:n.511-2489G>A (chr2-216991469-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 ENST00000447289.1(TESHL):n.511-2489G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 152,118 control chromosomes in the GnomAD database, including 19,250 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 0.48 ( 19250 hom., cov: 33)

Consequence

TESHL
ENST00000447289.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.38

Publications

5 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 = 0.732 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.511-2489G>A	intron_variant	Intron 3 of 3	5
TESHL	ENST00000607591.1 link	n.273-2489G>A	intron_variant	Intron 2 of 2	3
TESHL	ENST00000695932.1 link	n.449-2489G>A	intron_variant	Intron 2 of 11

Frequencies

GnomAD3 genomes

AF:

0.484

AC:

73555

AN:

152000

Hom.:

19213

Cov.:

show subpopulations

Gnomad AFR

AF:

0.671

Gnomad AMI

AF:

0.253

Gnomad AMR

AF:

0.501

Gnomad ASJ

AF:

0.376

Gnomad EAS

AF:

0.752

Gnomad SAS

AF:

0.525

Gnomad FIN

AF:

0.297

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.381

Gnomad OTH

AF:

0.474

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

GnomAD4 genome

AF:

0.484

AC:

73642

AN:

152118

Hom.:

19250

Cov.:

AF XY:

0.484

AC XY:

35992

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.671

AC:

27868

AN:

41510

American (AMR)

AF:

0.502

AC:

7678

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.376

AC:

1306

AN:

3472

East Asian (EAS)

AF:

0.752

AC:

3890

AN:

5174

South Asian (SAS)

AF:

0.523

AC:

2519

AN:

4814

European-Finnish (FIN)

AF:

0.297

AC:

3131

AN:

10558

Middle Eastern (MID)

AF:

0.384

AC:

113

AN:

294

European-Non Finnish (NFE)

AF:

0.381

AC:

25913

AN:

67980

Other (OTH)

AF:

0.471

AC:

994

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1786

3573

5359

7146

8932

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

644

1288

1932

2576

3220

<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:

0.415

Hom.:

21642

Bravo

AF:

0.508

Asia WGS

AF:

0.632

AC:

2198

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.85

(source)

DANN

Benign

0.58

PhyloP100

-1.4

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