rs6739040

Variant names:

• chr2-217087003-A-G
• rs6739040
• ENST00000695932.1:n.509+92985A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-217087003-A-G
• chr2-217087003-A-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+92985A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,210 control chromosomes in the GnomAD database, including 1,548 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 0.12 (1548 hom., cov: 32)
• Consequence: TESHL ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TESHL	ENST00000695932.1		n.509+92985A>G		intron	N/A
	TESHL	ENST00000695934.1		n.173-66408A>G		intron	N/A
	ENSG00000287498	ENST00000802626.1		n.296+4912T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18172 AN: 152092 Hom.: 1544 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0977

Gnomad ASJ AF: 0.0885

Gnomad EAS AF: 0.0260

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0256

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0718

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.120 AC: 18207 AN: 152210 Hom.: 1548 Cov.: 32 AF XY: 0.117 AC XY: 8697 AN XY: 74420

African (AFR) AF: 0.239 AC: 9906 AN: 41496

American (AMR) AF: 0.0974 AC: 1491 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0885 AC: 307 AN: 3468

East Asian (EAS) AF: 0.0261 AC: 135 AN: 5180

South Asian (SAS) AF: 0.172 AC: 830 AN: 4820

European-Finnish (FIN) AF: 0.0256 AC: 272 AN: 10616

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0718 AC: 4881 AN: 68010

Other (OTH) AF: 0.120 AC: 253 AN: 2112

Alfa AF: 0.0813 Hom.: 1985

Bravo AF: 0.127

Asia WGS AF: 0.122 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.75
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs6739040; hg19: chr2-217951726;