chr2-217258925-G-A

Variant names:

• chr2-217258925-G-A
• rs2553026
• ENST00000695932.1:n.510-2735G>A

Variant summary

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

The ENST00000695932.1(TESHL):​n.510-2735G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 151,988 control chromosomes in the GnomAD database, including 25,191 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 0.53 (25191 hom., cov: 31)
• Consequence: TESHL ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 12 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.716 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TESHL	ENST00000695932.1		n.510-2735G>A		intron	N/A
	TESHL	ENST00000695934.1		n.714-379G>A		intron	N/A
	TESHL	ENST00000695940.1		n.581-379G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79821 AN: 151872 Hom.: 25188 Cov.: 31

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.525 AC: 79835 AN: 151988 Hom.: 25191 Cov.: 31 AF XY: 0.520 AC XY: 38619 AN XY: 74290

African (AFR) AF: 0.178 AC: 7370 AN: 41470

American (AMR) AF: 0.598 AC: 9151 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1838 AN: 3466

East Asian (EAS) AF: 0.262 AC: 1349 AN: 5140

South Asian (SAS) AF: 0.545 AC: 2620 AN: 4810

European-Finnish (FIN) AF: 0.633 AC: 6679 AN: 10550

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 49020 AN: 67946

Other (OTH) AF: 0.543 AC: 1146 AN: 2112

Alfa AF: 0.631 Hom.: 64541

Bravo AF: 0.508

Asia WGS AF: 0.388 AC: 1351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.8
DANN	Benign	0.85
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2553026; hg19: chr2-218123648;