ENST00000695932.1:n.509+79436G>A

Variant names:

• chr2-217073454-G-A
• rs13011060
• ENST00000695932.1:n.509+79436G>A

Variant summary

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

The ENST00000695932.1(TESHL):​n.509+79436G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,094 control chromosomes in the GnomAD database, including 4,838 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 0.24 (4838 hom., cov: 31)
• Consequence: TESHL ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 3 publications found

Genes affected

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

ENSG00000287498 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 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+79436G>A		intron_variant	Intron 3 of 11
TESHL	ENST00000695934.1	n.172+79436G>A		intron_variant	Intron 3 of 8
ENSG00000287498	ENST00000802626.1	n.297-8440C>T		intron_variant	Intron 3 of 5
ENSG00000287498	ENST00000802627.1	n.210-8440C>T		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36858 AN: 151976 Hom.: 4826 Cov.: 31

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.0763

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.243 AC: 36894 AN: 152094 Hom.: 4838 Cov.: 31 AF XY: 0.235 AC XY: 17441 AN XY: 74370

African (AFR) AF: 0.315 AC: 13069 AN: 41464

American (AMR) AF: 0.200 AC: 3057 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 955 AN: 3472

East Asian (EAS) AF: 0.0761 AC: 393 AN: 5162

South Asian (SAS) AF: 0.172 AC: 829 AN: 4816

European-Finnish (FIN) AF: 0.142 AC: 1504 AN: 10594

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16292 AN: 67986

Other (OTH) AF: 0.248 AC: 523 AN: 2112

Alfa AF: 0.222 Hom.: 3587

Bravo AF: 0.249

Asia WGS AF: 0.154 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.58
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs13011060; hg19: chr2-217938177;