dbSNP rs1921987: TESHL:n.511-36768G>A (chr2-216957190-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.511-36768G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,954 control chromosomes in the GnomAD database, including 8,372 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 0.31 ( 8372 hom., cov: 31)

Consequence

TESHL
ENST00000447289.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.467

Publications

0 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=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 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.511-36768G>A	intron_variant	Intron 3 of 3	5
TESHL	ENST00000607591.1 link	n.114-24781G>A	intron_variant	Intron 1 of 2	3
TESHL	ENST00000695932.1 link	n.449-36768G>A	intron_variant	Intron 2 of 11

Frequencies

GnomAD3 genomes

AF:

0.313

AC:

47493

AN:

151838

Hom.:

8374

Cov.:

show subpopulations

Gnomad AFR

AF:

0.150

Gnomad AMI

AF:

0.371

Gnomad AMR

AF:

0.361

Gnomad ASJ

AF:

0.345

Gnomad EAS

AF:

0.233

Gnomad SAS

AF:

0.490

Gnomad FIN

AF:

0.374

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.382

Gnomad OTH

AF:

0.322

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

GnomAD4 genome

AF:

0.313

AC:

47497

AN:

151954

Hom.:

8372

Cov.:

AF XY:

0.317

AC XY:

23562

AN XY:

74260

show subpopulations

African (AFR)

AF:

0.150

AC:

6204

AN:

41460

American (AMR)

AF:

0.361

AC:

5516

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.345

AC:

1196

AN:

3468

East Asian (EAS)

AF:

0.234

AC:

1204

AN:

5154

South Asian (SAS)

AF:

0.490

AC:

2358

AN:

4812

European-Finnish (FIN)

AF:

0.374

AC:

3942

AN:

10538

Middle Eastern (MID)

AF:

0.364

AC:

107

AN:

294

European-Non Finnish (NFE)

AF:

0.382

AC:

25949

AN:

67938

Other (OTH)

AF:

0.323

AC:

683

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1602

3204

4805

6407

8009

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

490

980

1470

1960

2450

<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:

0.361

Hom.:

5625

Bravo

AF:

0.301

Asia WGS

AF:

0.358

AC:

1243

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

4.0

(source)

DANN

Benign

0.75

PhyloP100

0.47

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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