ENST00000695932.1:n.509+50722G>A

Variant names:

• chr2-217044740-G-A
• rs6721996
• ENST00000695932.1:n.509+50722G>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+50722G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,964 control chromosomes in the GnomAD database, including 19,190 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 0.49 (19190 hom., cov: 33)
• Consequence: TESHL ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156
• Publications: 15 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 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+50722G>A		intron	N/A
	TESHL	ENST00000695934.1		n.172+50722G>A		intron	N/A
	TESHL	ENST00000695937.1		n.289+7460G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74648 AN: 151844 Hom.: 19166 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.492 AC: 74714 AN: 151964 Hom.: 19190 Cov.: 33 AF XY: 0.493 AC XY: 36633 AN XY: 74254

African (AFR) AF: 0.393 AC: 16263 AN: 41426

American (AMR) AF: 0.600 AC: 9153 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1622 AN: 3472

East Asian (EAS) AF: 0.901 AC: 4657 AN: 5166

South Asian (SAS) AF: 0.490 AC: 2359 AN: 4818

European-Finnish (FIN) AF: 0.484 AC: 5103 AN: 10544

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 34006 AN: 67960

Other (OTH) AF: 0.508 AC: 1071 AN: 2108

Alfa AF: 0.489 Hom.: 15539

Bravo AF: 0.500

Asia WGS AF: 0.726 AC: 2521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.37
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs6721996; hg19: chr2-217909463;