ENST00000456163.2:n.89-1903G>A

Variant names:

• chr2-216868773-G-A
• rs1922005
• ENST00000456163.2:n.89-1903G>A

Variant summary

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

The ENST00000456163.2(TESHL):​n.89-1903G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456163.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TESHL	ENST00000456163.2	TSL:1	n.89-1903G>A		intron	N/A
	TESHL	ENST00000447289.1	TSL:5	n.510+103763G>A		intron	N/A
	TESHL	ENST00000451711.1	TSL:2	n.376-218G>A		intron	N/A

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

African (AFR) AF: 0.105 AC: 4359 AN: 41512

American (AMR) AF: 0.351 AC: 5356 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 857 AN: 3464

East Asian (EAS) AF: 0.520 AC: 2678 AN: 5152

South Asian (SAS) AF: 0.292 AC: 1408 AN: 4816

European-Finnish (FIN) AF: 0.188 AC: 1990 AN: 10590

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11532 AN: 67986

Other (OTH) AF: 0.232 AC: 490 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.33
DANN	Benign	0.61
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1922005; hg19: chr2-217733496;