2-216758526-T-G

Variant names:

• chr2-216758526-T-G
• rs737308
• ENST00000447289.1:n.389-6363T>G

Variant summary

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

The ENST00000447289.1(TESHL):​n.389-6363T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 152,094 control chromosomes in the GnomAD database, including 32,627 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 (32627 hom., cov: 33)
• Consequence: TESHL ENST00000447289.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.469
• 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=-0.82).
• 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.407-6363T>G		intron	N/A
	IGFBP-AS1	NR_187139.1		n.407-6363T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TESHL	ENST00000447289.1	TSL:5	n.389-6363T>G		intron	N/A
	TESHL	ENST00000695932.1		n.448+46057T>G		intron	N/A
	TESHL	ENST00000695934.1		n.111+46057T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98275 AN: 151976 Hom.: 32609 Cov.: 33

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.646 AC: 98327 AN: 152094 Hom.: 32627 Cov.: 33 AF XY: 0.642 AC XY: 47733 AN XY: 74342

African (AFR) AF: 0.508 AC: 21073 AN: 41472

American (AMR) AF: 0.623 AC: 9527 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2642 AN: 3472

East Asian (EAS) AF: 0.524 AC: 2703 AN: 5160

South Asian (SAS) AF: 0.701 AC: 3378 AN: 4818

European-Finnish (FIN) AF: 0.627 AC: 6620 AN: 10566

Middle Eastern (MID) AF: 0.723 AC: 211 AN: 292

European-Non Finnish (NFE) AF: 0.736 AC: 50075 AN: 68004

Other (OTH) AF: 0.691 AC: 1457 AN: 2110

Alfa AF: 0.687 Hom.: 4551

Bravo AF: 0.639

Asia WGS AF: 0.653 AC: 2271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.3
DANN	Benign	0.80
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs737308; hg19: chr2-217623249;