2-217041109-A-G

Variant names:

• chr2-217041109-A-G
• rs13387042
• XR_923878.3:n.7422A>G

Variant summary

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

The XR_923878.3(LOC105373874):​n.7422A>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 0.447 in 152,090 control chromosomes in the GnomAD database, including 16,742 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 0.45 (16742 hom., cov: 33)
• Consequence: LOC105373874 XR_923878.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 211 publications found

Genes affected

LOC105373874 (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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373874	XR_923878.3	n.7422A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TESHL	ENST00000695932.1	n.509+47091A>G		intron_variant	Intron 3 of 11
TESHL	ENST00000695934.1	n.172+47091A>G		intron_variant	Intron 3 of 8
TESHL	ENST00000695937.1	n.289+3829A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67955 AN: 151972 Hom.: 16718 Cov.: 33

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.447 AC: 68013 AN: 152090 Hom.: 16742 Cov.: 33 AF XY: 0.450 AC XY: 33417 AN XY: 74318

African (AFR) AF: 0.268 AC: 11127 AN: 41474

American (AMR) AF: 0.572 AC: 8736 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1559 AN: 3470

East Asian (EAS) AF: 0.902 AC: 4674 AN: 5182

South Asian (SAS) AF: 0.490 AC: 2365 AN: 4824

European-Finnish (FIN) AF: 0.476 AC: 5032 AN: 10582

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.486 AC: 33057 AN: 67960

Other (OTH) AF: 0.468 AC: 989 AN: 2114

Alfa AF: 0.477 Hom.: 81289

Bravo AF: 0.450

Asia WGS AF: 0.722 AC: 2508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.44
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs13387042; hg19: chr2-217905832;