rs1011502

Variant names:

• chr2-216943480-T-G
• rs1011502
• ENST00000447289.1:n.511-50478T>G

Variant summary

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

The ENST00000607591.1(TESHL):​n.114-38491T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 152,182 control chromosomes in the GnomAD database, including 8,793 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 (8793 hom., cov: 33)
• Consequence: TESHL ENST00000607591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.511
• Publications: 0 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607591.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TESHL	ENST00000447289.1	TSL:5	n.511-50478T>G		intron	N/A
	TESHL	ENST00000607591.1	TSL:3	n.114-38491T>G		intron	N/A
	TESHL	ENST00000695932.1		n.449-50478T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50565 AN: 152064 Hom.: 8785 Cov.: 33

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.332 AC: 50595 AN: 152182 Hom.: 8793 Cov.: 33 AF XY: 0.334 AC XY: 24879 AN XY: 74398

African (AFR) AF: 0.246 AC: 10228 AN: 41522

American (AMR) AF: 0.376 AC: 5757 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1064 AN: 3468

East Asian (EAS) AF: 0.265 AC: 1371 AN: 5174

South Asian (SAS) AF: 0.428 AC: 2064 AN: 4824

European-Finnish (FIN) AF: 0.360 AC: 3810 AN: 10584

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25274 AN: 67998

Other (OTH) AF: 0.337 AC: 712 AN: 2112

Alfa AF: 0.351 Hom.: 9651

Bravo AF: 0.328

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.3
DANN	Benign	0.66
PhyloP100		0.51

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1011502;

hg19: chr2-217808203;