rs1922005

chr2-216868773-G-Achr2-216868773-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000456163.2(TESHL):n.89-1903G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,086 control chromosomes in the GnomAD database, including 3,414 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 0.19 (3414 hom., cov: 32)
• Consequence: TESHL ENST00000456163.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

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

DIRC3-AS1 (HGNC:50636): (DIRC3 antisense RNA 1)

IGFBP-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGFBP-AS1	XR_001739169.1	n.11783+37291G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TESHL	ENST00000456163.2	n.89-1903G>A		intron_variant, non_coding_transcript_variant		1
DIRC3-AS1	ENST00000695932.1	n.449-125185G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28779 AN: 151968 Hom.: 3398 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.189 AC: 28820 AN: 152086 Hom.: 3414 Cov.: 32 AF XY: 0.196 AC XY: 14555 AN XY: 74344

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.232

Alfa AF: 0.0960 Hom.: 149

Bravo AF: 0.200

Asia WGS AF: 0.391 AC: 1356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.33
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1922005; hg19: chr2-217733496;