2-216763707-A-G

Variant names:

• chr2-216763707-A-G
• rs1861628
• ENST00000447289.1:n.389-1182A>G

Variant summary

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

The ENST00000447289.1(TESHL):​n.389-1182A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 152,028 control chromosomes in the GnomAD database, including 32,644 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 0.65 (32644 hom., cov: 32)
• Consequence: TESHL ENST00000447289.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 11 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.731 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.407-1182A>G		intron	N/A
	IGFBP-AS1	NR_187139.1		n.407-1182A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TESHL	ENST00000447289.1	TSL:5	n.389-1182A>G		intron	N/A
	TESHL	ENST00000695932.1		n.448+51238A>G		intron	N/A
	TESHL	ENST00000695934.1		n.111+51238A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98284 AN: 151910 Hom.: 32625 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.647 AC: 98336 AN: 152028 Hom.: 32644 Cov.: 32 AF XY: 0.642 AC XY: 47692 AN XY: 74280

African (AFR) AF: 0.509 AC: 21070 AN: 41426

American (AMR) AF: 0.623 AC: 9518 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2638 AN: 3470

East Asian (EAS) AF: 0.524 AC: 2710 AN: 5172

South Asian (SAS) AF: 0.705 AC: 3388 AN: 4808

European-Finnish (FIN) AF: 0.626 AC: 6609 AN: 10560

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50093 AN: 67992

Other (OTH) AF: 0.690 AC: 1455 AN: 2108

Alfa AF: 0.713 Hom.: 44237

Bravo AF: 0.639

Asia WGS AF: 0.654 AC: 2275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.52
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs1861628; hg19: chr2-217628430;