dbSNP rs1882420: TESHL:n.511-7172G>T (chr2-216986786-G-T) – 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.511-7172G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,046 control chromosomes in the GnomAD database, including 11,291 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 0.30 ( 11291 hom., cov: 32)

Consequence

TESHL
ENST00000447289.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.24

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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 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.511-7172G>T	intron_variant	Intron 3 of 3	5
TESHL	ENST00000607591.1 link	n.272+4657G>T	intron_variant	Intron 2 of 2	3
TESHL	ENST00000695932.1 link	n.449-7172G>T	intron_variant	Intron 2 of 11

Frequencies

GnomAD3 genomes

AF:

0.299

AC:

45352

AN:

151928

Hom.:

11249

Cov.:

show subpopulations

Gnomad AFR

AF:

0.679

Gnomad AMI

AF:

0.248

Gnomad AMR

AF:

0.263

Gnomad ASJ

AF:

0.113

Gnomad EAS

AF:

0.148

Gnomad SAS

AF:

0.143

Gnomad FIN

AF:

0.210

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.124

Gnomad OTH

AF:

0.258

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

GnomAD4 genome

AF:

0.299

AC:

45453

AN:

152046

Hom.:

11291

Cov.:

AF XY:

0.300

AC XY:

22262

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.680

AC:

28155

AN:

41424

American (AMR)

AF:

0.263

AC:

4026

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.113

AC:

391

AN:

3472

East Asian (EAS)

AF:

0.148

AC:

764

AN:

5176

South Asian (SAS)

AF:

0.142

AC:

684

AN:

4808

European-Finnish (FIN)

AF:

0.210

AC:

2221

AN:

10564

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.124

AC:

8400

AN:

68004

Other (OTH)

AF:

0.254

AC:

536

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1161

2322

3482

4643

5804

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.162

Hom.:

6246

Bravo

AF:

0.322

Asia WGS

AF:

0.181

AC:

628

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.13

(source)

DANN

Benign

0.66

PhyloP100

-2.2

Splicing

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

Publications

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rs1882420

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