dbSNP rs10169372: TESHL:n.509+12608A>G (chr2-217006626-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+12608A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0766 in 152,102 control chromosomes in the GnomAD database, including 1,218 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 0.077 ( 1218 hom., cov: 32)

Consequence

TESHL
ENST00000695932.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.762

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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 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+12608A>G	intron_variant	Intron 3 of 11
TESHL	ENST00000695934.1 link	n.172+12608A>G	intron_variant	Intron 3 of 8
TESHL	ENST00000695937.1 link	n.221+12608A>G	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.0764

AC:

11619

AN:

151984

Hom.:

1216

Cov.:

show subpopulations

Gnomad AFR

AF:

0.240

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0341

Gnomad ASJ

AF:

0.0303

Gnomad EAS

AF:

0.0386

Gnomad SAS

AF:

0.0510

Gnomad FIN

AF:

0.00151

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.00694

Gnomad OTH

AF:

0.0586

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

GnomAD4 genome

AF:

0.0766

AC:

11650

AN:

152102

Hom.:

1218

Cov.:

AF XY:

0.0744

AC XY:

5529

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.240

AC:

9956

AN:

41430

American (AMR)

AF:

0.0340

AC:

520

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0303

AC:

105

AN:

3470

East Asian (EAS)

AF:

0.0383

AC:

198

AN:

5168

South Asian (SAS)

AF:

0.0507

AC:

244

AN:

4816

European-Finnish (FIN)

AF:

0.00151

AC:

AN:

10608

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00694

AC:

472

AN:

68020

Other (OTH)

AF:

0.0570

AC:

120

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

482

963

1445

1926

2408

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

224

336

448

560

<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:

0.0352

Hom.:

153

Bravo

AF:

0.0859

Asia WGS

AF:

0.0510

AC:

178

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.2

(source)

DANN

Benign

0.60

PhyloP100

0.76

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