ENST00000447289.1:n.389-17291A>C

Variant names:

• chr2-216747598-A-C
• rs7568039
• ENST00000447289.1:n.389-17291A>C

Variant summary

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

The ENST00000447289.1(TESHL):​n.389-17291A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 152,098 control chromosomes in the GnomAD database, including 33,632 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 0.66 (33632 hom., cov: 32)
• Consequence: TESHL ENST00000447289.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.601
• Publications: 6 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=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.733 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.407-17291A>C		intron	N/A
	IGFBP-AS1	NR_187139.1		n.407-17291A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TESHL	ENST00000447289.1	TSL:5	n.389-17291A>C		intron	N/A
	TESHL	ENST00000695932.1		n.448+35129A>C		intron	N/A
	TESHL	ENST00000695934.1		n.111+35129A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99905 AN: 151980 Hom.: 33610 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.657 AC: 99957 AN: 152098 Hom.: 33632 Cov.: 32 AF XY: 0.654 AC XY: 48597 AN XY: 74320

African (AFR) AF: 0.520 AC: 21550 AN: 41470

American (AMR) AF: 0.678 AC: 10355 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2692 AN: 3470

East Asian (EAS) AF: 0.546 AC: 2829 AN: 5178

South Asian (SAS) AF: 0.705 AC: 3398 AN: 4822

European-Finnish (FIN) AF: 0.624 AC: 6598 AN: 10566

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.738 AC: 50206 AN: 67986

Other (OTH) AF: 0.700 AC: 1481 AN: 2116

Alfa AF: 0.595 Hom.: 1768

Bravo AF: 0.653

Asia WGS AF: 0.664 AC: 2312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	2.6
DANN	Benign	0.91
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs7568039; hg19: chr2-217612321;