chr2-217056046-G-T

Variant names:

• chr2-217056046-G-T
• rs4442975
• ENST00000695932.1:n.509+62028G>T

Variant summary

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

The ENST00000695932.1(TESHL):​n.509+62028G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 152,064 control chromosomes in the GnomAD database, including 18,526 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 0.48 (18526 hom., cov: 33)
• Consequence: TESHL ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 47 publications found

Genes affected

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

ENSG00000304367 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TESHL	ENST00000695932.1	n.509+62028G>T		intron_variant	Intron 3 of 11
TESHL	ENST00000695934.1	n.172+62028G>T		intron_variant	Intron 3 of 8
ENSG00000304367	ENST00000802915.1	n.247+7756G>T		intron_variant	Intron 1 of 1
TESHL	ENST00000695937.1	n.*82G>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72615 AN: 151946 Hom.: 18501 Cov.: 33

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.478 AC: 72681 AN: 152064 Hom.: 18526 Cov.: 33 AF XY: 0.479 AC XY: 35608 AN XY: 74362

African (AFR) AF: 0.344 AC: 14269 AN: 41466

American (AMR) AF: 0.599 AC: 9150 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1614 AN: 3470

East Asian (EAS) AF: 0.895 AC: 4640 AN: 5186

South Asian (SAS) AF: 0.488 AC: 2350 AN: 4818

European-Finnish (FIN) AF: 0.479 AC: 5060 AN: 10568

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34059 AN: 67968

Other (OTH) AF: 0.500 AC: 1057 AN: 2116

Alfa AF: 0.494 Hom.: 35691

Bravo AF: 0.484

Asia WGS AF: 0.725 AC: 2518 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.051
DANN	Benign	0.26
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs4442975; hg19: chr2-217920769;