rs13016130

Variant names:

• chr2-217109554-G-T
• rs13016130
• ENST00000695932.1:n.509+115536G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000695932.1(TESHL):​n.509+115536G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 151,950 control chromosomes in the GnomAD database, including 10,794 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 0.34 (10794 hom., cov: 31)
• Consequence: TESHL ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 3 publications found

Genes affected

TESHL (HGNC:52740): (testicular germ cell expressed HSF2 interacting lncRNA)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TESHL	ENST00000695932.1	n.509+115536G>T		intron_variant	Intron 3 of 11
TESHL	ENST00000695934.1	n.173-43857G>T		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52163 AN: 151830 Hom.: 10790 Cov.: 31

Gnomad AFR AF: 0.0976

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.343 AC: 52173 AN: 151950 Hom.: 10794 Cov.: 31 AF XY: 0.347 AC XY: 25760 AN XY: 74236

African (AFR) AF: 0.0974 AC: 4038 AN: 41470

American (AMR) AF: 0.463 AC: 7064 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1473 AN: 3470

East Asian (EAS) AF: 0.364 AC: 1874 AN: 5144

South Asian (SAS) AF: 0.392 AC: 1885 AN: 4804

European-Finnish (FIN) AF: 0.436 AC: 4601 AN: 10546

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30053 AN: 67934

Other (OTH) AF: 0.369 AC: 781 AN: 2114

Alfa AF: 0.395 Hom.: 1754

Bravo AF: 0.336

Asia WGS AF: 0.355 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.80
DANN	Benign	0.52
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs13016130; hg19: chr2-217974277;