ENST00000695932.1:n.509+26918C>T

Variant names:

• chr2-217020936-C-T
• rs10177578
• ENST00000695932.1:n.509+26918C>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+26918C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 151,932 control chromosomes in the GnomAD database, including 39,698 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 0.72 (39698 hom., cov: 32)
• Consequence: TESHL ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 4 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000695932.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TESHL	ENST00000695932.1		n.509+26918C>T		intron	N/A
	TESHL	ENST00000695934.1		n.172+26918C>T		intron	N/A
	TESHL	ENST00000695937.1		n.222-16277C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.718 AC: 108945 AN: 151814 Hom.: 39647 Cov.: 32

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.718 AC: 109053 AN: 151932 Hom.: 39698 Cov.: 32 AF XY: 0.716 AC XY: 53192 AN XY: 74264

African (AFR) AF: 0.825 AC: 34232 AN: 41500

American (AMR) AF: 0.734 AC: 11208 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2284 AN: 3470

East Asian (EAS) AF: 0.934 AC: 4841 AN: 5184

South Asian (SAS) AF: 0.717 AC: 3449 AN: 4812

European-Finnish (FIN) AF: 0.630 AC: 6637 AN: 10532

Middle Eastern (MID) AF: 0.702 AC: 205 AN: 292

European-Non Finnish (NFE) AF: 0.651 AC: 44171 AN: 67852

Other (OTH) AF: 0.700 AC: 1471 AN: 2100

Alfa AF: 0.672 Hom.: 121249

Bravo AF: 0.735

Asia WGS AF: 0.855 AC: 2940 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.69
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs10177578; hg19: chr2-217885659;