2-216760800-G-A

Variant names:

• chr2-216760800-G-A
• rs13015993
• ENST00000447289.1:n.389-4089G>A

Variant summary

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

The ENST00000447289.1(TESHL):​n.389-4089G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 151,986 control chromosomes in the GnomAD database, including 32,360 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 0.64 (32360 hom., cov: 32)
• Consequence: TESHL ENST00000447289.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.563
• Publications: 25 publications found

Genes affected

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

IGFBP-AS1 (HGNC:55655): (IGFBP5 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447289.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGFBP-AS1	NR_187138.1		n.407-4089G>A		intron	N/A
	IGFBP-AS1	NR_187139.1		n.407-4089G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TESHL	ENST00000447289.1	TSL:5	n.389-4089G>A		intron	N/A
	TESHL	ENST00000695932.1		n.448+48331G>A		intron	N/A
	TESHL	ENST00000695934.1		n.111+48331G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97873 AN: 151866 Hom.: 32340 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.644 AC: 97928 AN: 151986 Hom.: 32360 Cov.: 32 AF XY: 0.640 AC XY: 47501 AN XY: 74262

African (AFR) AF: 0.508 AC: 21051 AN: 41438

American (AMR) AF: 0.621 AC: 9485 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2631 AN: 3470

East Asian (EAS) AF: 0.522 AC: 2689 AN: 5148

South Asian (SAS) AF: 0.703 AC: 3371 AN: 4798

European-Finnish (FIN) AF: 0.625 AC: 6590 AN: 10548

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.733 AC: 49805 AN: 67982

Other (OTH) AF: 0.688 AC: 1452 AN: 2110

Alfa AF: 0.704 Hom.: 150173

Bravo AF: 0.637

Asia WGS AF: 0.652 AC: 2269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.52
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs13015993; hg19: chr2-217625523;