chr2-217091812-A-G

Variant names:

• chr2-217091812-A-G
• rs13013872
• ENST00000803105.1:n.230A>G

Variant summary

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

The ENST00000803105.1(ENSG00000304387):​n.230A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 148,878 control chromosomes in the GnomAD database, including 30,594 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 0.61 (30594 hom., cov: 31)
• Consequence: ENSG00000304387 ENST00000803105.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 2 publications found

Genes affected

ENSG00000304387 (HGNC:):

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803105.1. 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
	ENSG00000304387	ENST00000803105.1		n.230A>G		non_coding_transcript_exon	Exon 2 of 2
	TESHL	ENST00000695932.1		n.509+97794A>G		intron	N/A
	TESHL	ENST00000695934.1		n.173-61599A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.614 AC: 91287 AN: 148762 Hom.: 30551 Cov.: 31

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.614 AC: 91389 AN: 148878 Hom.: 30594 Cov.: 31 AF XY: 0.608 AC XY: 44222 AN XY: 72760

African (AFR) AF: 0.794 AC: 31077 AN: 39138

American (AMR) AF: 0.649 AC: 9837 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1826 AN: 3444

East Asian (EAS) AF: 0.411 AC: 2118 AN: 5152

South Asian (SAS) AF: 0.577 AC: 2753 AN: 4774

European-Finnish (FIN) AF: 0.446 AC: 4662 AN: 10446

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.552 AC: 37256 AN: 67482

Other (OTH) AF: 0.605 AC: 1263 AN: 2086

Alfa AF: 0.655 Hom.: 8975

Bravo AF: 0.639

Asia WGS AF: 0.517 AC: 1798 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.77
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs13013872; hg19: chr2-217956535;