chr2-217079904-A-C

Variant names:

• chr2-217079904-A-C
• rs7579306
• ENST00000695932.1:n.509+85886A>C

Variant summary

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

The ENST00000695932.1(TESHL):​n.509+85886A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,008 control chromosomes in the GnomAD database, including 8,598 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 0.32 (8598 hom., cov: 32)
• Consequence: TESHL ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 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+85886A>C		intron_variant	Intron 3 of 11
TESHL	ENST00000695934.1	n.173-73507A>C		intron_variant	Intron 3 of 8
ENSG00000287498	ENST00000802626.1	n.296+12011T>G		intron_variant	Intron 3 of 5
ENSG00000287498	ENST00000802627.1	n.209+12011T>G		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49107 AN: 151890 Hom.: 8575 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.323 AC: 49160 AN: 152008 Hom.: 8598 Cov.: 32 AF XY: 0.322 AC XY: 23936 AN XY: 74296

African (AFR) AF: 0.446 AC: 18483 AN: 41448

American (AMR) AF: 0.322 AC: 4921 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 886 AN: 3470

East Asian (EAS) AF: 0.112 AC: 579 AN: 5172

South Asian (SAS) AF: 0.344 AC: 1653 AN: 4800

European-Finnish (FIN) AF: 0.269 AC: 2840 AN: 10554

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18822 AN: 67994

Other (OTH) AF: 0.311 AC: 654 AN: 2100

Alfa AF: 0.283 Hom.: 11659

Bravo AF: 0.330

Asia WGS AF: 0.204 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.57
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs7579306; hg19: chr2-217944627;