2-217059671-G-A

Variant names:

• chr2-217059671-G-A
• rs13000023
• ENST00000695932.1:n.509+65653G>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+65653G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,150 control chromosomes in the GnomAD database, including 2,987 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 0.19 (2987 hom., cov: 32)
• Consequence: TESHL ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563
• Publications: 7 publications found

Genes affected

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

ENSG00000304367 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.229 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+65653G>A		intron	N/A
	TESHL	ENST00000695934.1		n.172+65653G>A		intron	N/A
	ENSG00000304367	ENST00000802915.1		n.248-6031G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29043 AN: 152032 Hom.: 2978 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.0829

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.191 AC: 29063 AN: 152150 Hom.: 2987 Cov.: 32 AF XY: 0.185 AC XY: 13772 AN XY: 74370

African (AFR) AF: 0.150 AC: 6243 AN: 41514

American (AMR) AF: 0.183 AC: 2795 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3468

East Asian (EAS) AF: 0.0829 AC: 429 AN: 5178

South Asian (SAS) AF: 0.175 AC: 842 AN: 4814

European-Finnish (FIN) AF: 0.135 AC: 1429 AN: 10584

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15743 AN: 67980

Other (OTH) AF: 0.207 AC: 436 AN: 2110

Alfa AF: 0.210 Hom.: 1990

Bravo AF: 0.191

Asia WGS AF: 0.136 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.50
DANN	Benign	0.55
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs13000023; hg19: chr2-217924394;