dbSNP rs1922005: TESHL:n.89-1903G>A (chr2-216868773-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 ENST00000456163.2(TESHL):n.89-1903G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,086 control chromosomes in the GnomAD database, including 3,414 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 0.19 ( 3414 hom., cov: 32)

Consequence

TESHL
ENST00000456163.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.01

Publications

3 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.503 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	ENST00000456163.2 link	n.89-1903G>A	intron_variant	Intron 1 of 2	1
TESHL	ENST00000447289.1 link	n.510+103763G>A	intron_variant	Intron 3 of 3	5
TESHL	ENST00000451711.1 link	n.376-218G>A	intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes

AF:

0.189

AC:

28779

AN:

151968

Hom.:

3398

Cov.:

show subpopulations

Gnomad AFR

AF:

0.105

Gnomad AMI

AF:

0.0822

Gnomad AMR

AF:

0.350

Gnomad ASJ

AF:

0.247

Gnomad EAS

AF:

0.519

Gnomad SAS

AF:

0.292

Gnomad FIN

AF:

0.188

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.170

Gnomad OTH

AF:

0.226

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

GnomAD4 genome

AF:

0.189

AC:

28820

AN:

152086

Hom.:

3414

Cov.:

AF XY:

0.196

AC XY:

14555

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.105

AC:

4359

AN:

41512

American (AMR)

AF:

0.351

AC:

5356

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.247

AC:

857

AN:

3464

East Asian (EAS)

AF:

0.520

AC:

2678

AN:

5152

South Asian (SAS)

AF:

0.292

AC:

1408

AN:

4816

European-Finnish (FIN)

AF:

0.188

AC:

1990

AN:

10590

Middle Eastern (MID)

AF:

0.255

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.170

AC:

11532

AN:

67986

Other (OTH)

AF:

0.232

AC:

490

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1114

2228

3342

4456

5570

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

314

628

942

1256

1570

<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:

0.0960

Hom.:

149

Bravo

AF:

0.200

Asia WGS

AF:

0.391

AC:

1356

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.33

(source)

DANN

Benign

0.61

PhyloP100

-1.0

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