rs2068218

Variant names:

• chr2-217108725-G-A
• rs2068218
• ENST00000695932.1:n.509+114707G>A

Variant summary

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

The ENST00000695932.1(TESHL):​n.509+114707G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,104 control chromosomes in the GnomAD database, including 10,781 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 0.33 (10781 hom., cov: 32)
• Consequence: TESHL ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• Publications: 6 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 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+114707G>A		intron_variant	Intron 3 of 11
TESHL	ENST00000695934.1	n.173-44686G>A		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49717 AN: 151986 Hom.: 10753 Cov.: 32

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0612

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.327 AC: 49788 AN: 152104 Hom.: 10781 Cov.: 32 AF XY: 0.318 AC XY: 23648 AN XY: 74358

African (AFR) AF: 0.621 AC: 25728 AN: 41448

American (AMR) AF: 0.195 AC: 2980 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 652 AN: 3468

East Asian (EAS) AF: 0.0609 AC: 316 AN: 5186

South Asian (SAS) AF: 0.161 AC: 776 AN: 4812

European-Finnish (FIN) AF: 0.205 AC: 2170 AN: 10578

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16305 AN: 68006

Other (OTH) AF: 0.273 AC: 575 AN: 2110

Alfa AF: 0.256 Hom.: 9299

Bravo AF: 0.338

Asia WGS AF: 0.164 AC: 575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.71
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs2068218; hg19: chr2-217973448;